Well, I went and made myself a Focused Transmuter... Looking at the Handy Links, I must admit I had been quite surprised there was no guide to Transmutation spells! Considering that Transmutation and Conjuration are the 2 most powerful and versatile wizard schools, it's a shame. So, after going through almost every book printed, here it is, finally.
In case you're wondering, yes, it's very much possible to play a Focused Specialist (Transmuter) at all levels. It's about as good as a Focused Conjurer.
The Rating System
Unabashedly stolen from TM, the rating system follows.
: This spell's a turkey; not worth having in your spellbook at all.
:thumbsdow : Not bad, but not good enough for me to recommend.
* : Run of the mill. It's OK, but nothing special.
: The spell is solid. I recommend it.
: This spell is highly recommended.
:evillaugh : Jackpot!
Enlarge Person (:evillaugh) - Gives your Fighter Reach, so he can kill things better. If you didn't get it by now, that's your job: letting the Big Stupid Fighter kill things. Nerveskitter[sup]SpC[/sup] (:evillaugh) - It helps you win Initiative. That's pure WIN, right there! Treacherous Weapon[sup]ExEv[/sup] (:plotting - Save negates, but not only does it scale until 9th level, it can be cast as either an Immediate Action or a Standard Action - which doubles the effect. Awesome spell. Ray of Clumsiness[sup]SpC[/sup] (:plotting - It's Ray of Enfeeblement, except instead of weakening offense, it hurts their defense. Really nice spell, easily lowering AC and Reflex saves. Kill those pesky Rogues with this.
Expeditious Retreat (+Swift)[sup]PHB/SpC[/sup] (:thumbsup - It's a spell for running away. You have a d4 HD. Guess what you do when your Big Stupid Fighter fails?
Hoard Gullet[sup]DrM[/sup] (:thumbsup - How about a Bag of Holding... at level 1? Sure, it's not perfect, but it's a good spell to know.
Snuff the Light[sup]DotU[/sup] (:thumbsup - I'm sure you can see the use of turning off the lights as a Swift Action...
Reduce Person (*) - It adds to your AC and some skills. Not bad, but barely worth a slot.
Feather Fall (*) - Like Magic Missile, it's a spell every Wizard knows. It's a handy little thing to have, but somehow the others live without it.
Magic Weapon (:thumbsdow) - Only ever of any use when facing DR and Incorporeal enemies, this is a fairly useless spell. At low levels, you don't need it; At high levels, you have Greater Magic Weapon.
Alter Self (evillaugh:evillaugh) - This spell deserves a whole thread. I don't recommend you use it, but it's power is undeniable.
Quick Potion[sup]SpC[/sup] (:evillaugh) - Not only does this allow you to save actions in combat and let the peons act in your stead, it can be used to store emergency healing potions and the like. Also, these potions aren't made at minimum CL. A fun trick with this is making the Material Component for Tenser's Transformation and it's derivatives.
Jaws of the Moray[sup]Storm[/sup] (:evillaugh) - It gives the BSF an extra attack per round. It's no Haste, but it's good. Not only that, but it's kinda like Improved Grab.
Levitate (:evillaugh) - That's like flight, except you can't move as easily. If they can't reach you, they can't hurt you.
Rope Trick (:plotting - This is your safe haven spell. Use it well, grasshopper.
Heroics[sup]SpC[/sup] (:plotting - Again, your job is making the fighter able to better smash things. This spell does that nicely.
Swift Fly[sup]SpC[/sup] (:thumbsup - That's Fly, 1 level early. Useful for running away, covering distances or along with other spells (Levitate/Greater Floating Disc), getting actual flight. If you're an actual Transmuter, this is a (:turkey, because you can get Sudden Shift.
Fox's Cunning (:thumbsup - I only mention this spell because of a trick related to Quick Potion and Mental Pinnacle. Without it, it's not a very good spell except for raising DC at low levels.
Knock (*) - Opening doors is not your job. The rogue can pick them and the barbarian can smash them, but if you want a quick, easy, assured and simply enchanting entrance, use this. It makes rogues cry.
Heart of Air[sup]CM[/sup] (:thumbsdow) - You want this spell for the combo with other Heart of... spells, but little else.
Haste (:evillaugh) - Get this one on your allies, and you make them that much deadlier.
Slow (:evillaugh) - Get this one on your foes, and you basically win.
Fly (:evillaugh) - You can fly! No more of this "walking" mere mortals do!
Celestial Aspect[sup]BoED[/sup] - (:evillaugh/:plotting If you can get someone to cure the ability damage, it's plain out better than Fly, and offers other options, to boot. If not, it's still rather good.
Shrink Item (:plotting - You can use this spell to carry around bonfires, statues, boulders, corpses, or just about anything else. Not only can you break the game with this, you can pillage and loot anything not nailed down.
Greater Magic Weapon (:plotting - Give your allies +5 weapons. They'll thank you for it more than if you'd cast another Fireball.
Heart of Water[sup]CM[/sup] (:plotting - Remember the days when not being able to cast Freedom of Movement was a weakness of Wizards? Now you can cast it, and better than any Cleric ever could.
Greater Mighty Wallop[sup]RotD[/sup] (:plotting - HUGE damage boosts to your allies.
Halt[sup]PHB2[/sup] (:plotting - Immediate Action debuff. Very nice.
Dragonskin[sup]SpC[/sup] (:thumbsup - This is mostly nice to get Energy Resistance, but the NA doesn't hurt, either.
Dolorous Blow[sup]SpC[/sup] (:thumbsup - Give the BSF Imp. Critical and Automatic Confirmation. That's pretty cool.
Mass Snake's Swiftness[sup]SpC[/sup] (:thumbsup - Not everyone uses Haste well. A Swift Hunter might prefer this, for instance. Also useful if your foes move around a lot or there are a lot weak ones.
Animate Weapon[sup]CM[/sup] (:thumbsup - The effect depends on the size of the weapon, not you. Have the BSF carry a spiked chain that wouldn't shame a titan. Might be slightly broken if you use it like that, but it's plain useless otherwise.
Sense of the Dragon[sup]RotD[/sup] (*) - It's essentially Blindsense 30', which is always good to have.
Control Temperature[sup]Frost[/sup] (*) - This is your Endure Elements, except you can use it for so much more. Not bad.
Wand Modulation[sup]CS[/sup] (:thumbsdow) - You might need the same spell a lot of times at once, and this allows for it, but it's hardly cost-effective.
Siphon[sup]CS[/sup] (:turkey - This one is nice if you have an URGENT need for spells, but it's really expensive to use, unless you have a Staff of the Magi.
Polymorph (evillaugh:evillaugh) - You win. No save to avoid awesome. Probably one of the most broken and open ended spells ever. If your type isn't Humanoid, it gets just as silly earlier.
Displacer Form[sup]SpC[/sup] (:evillaugh) - Not only is this a decent combat form, but you also get Displacement (yes, this is a Trans spell, not an Illusion), and you get to keep your casting!
Celerity[sup]PHB2[/sup] (:evillaugh) - You can act out of turn. That's so powerful, it's silly.
Heart of Earth[sup]CM[/sup] (:evillaugh) - Stoneskin for free, as well as Temp HP and synergy bonuses? Great value.
Perfect Summons[sup]BoED[/sup] (:evillaugh) - At this point, you'll be meeting lots of spellcasters, demons and devils. Guess what those guys do? This gets you free, powerful, allies.
Voice of the Dragon[sup]SpC[/sup] (:plotting - You're not the party face, but you can cast Suggestion! Considering you've probably prohibited Enchantment, this is good.
Trollshape[sup]PHB2[/sup] (:plotting - This gives you Regeneration. Enough said. It's a defensive spell, and a good one.
Spell Enhancer[sup]SpC[/sup] (:plotting - Pretty darned nice. When casting CL dependent spells, this is amazing. Use it to get the good kind of Phantasmal Steed, for instance.
Baleful Blink[sup]PHB2[/sup] (:plotting - Save or lose 50% of your actions? Nice!
Passage of the Shifting Sands[sup]DrM[/sup] (:plotting - Very nice getaway spell, it gives you decent speed, and an attack capacity.
Mnemonic Enhancer (:thumbsup - Adds some versatility, and if you have a day in advance, you can get free spells.
Call of Stone[sup]PHB2[/sup] (:thumbsup - Wierd sort of Slow, and given a high DC and CL, it might well be a SoD.
Stone Shape (*) - Pretty darned useful in natural terrain and stone walls.
Repair Critical Damage[sup]SpC[/sup] (*) - You're no healer, that's for sure, but if you have a Warforged ally, this spell and lessers are useful.
Alliance Undone[sup]ExEv[/sup] (*) - This one removes all "alliance" bonuses with no save, in a large area. Bardic Music? Marshal Auras? Flanking? None of that, and more. Mostly useful against a party, hence the lowish rating.
Mark of the Enlightened Soul[sup]DrM[/sup] (*) - Regeneration/Good exists, and with this spell you can bypass it and get free Empowered spells. Not bad, I think, but this is for those rare times you blast.
Scramble Portal[sup]SpC[/sup] (:thumbsdow) - Only ever of use in a planar campaign or the like. Screw over Gates with this.
Draconic Polymorph[sup]Draconomicon[/sup] (evillaugh:evillaugh) - This is Polymorph, except improved in every way that matters! If you thought Polymorph was broken (it probably is...), then don't even look at this spell.
Telekinesis (:evillaugh) - You can grapple Ghosts with this, damnit!
Mass Fly[sup]SpC[/sup] (:evillaugh) - This spell will win you encounters against earthbound foes without a doubt. It's even rather good for aerial combat. LEARN THIS.
Lord of the Sky[sup]DrM[/sup] (:evillaugh) - I love this spell! You're a Wizard, so a good assumption is that you don't walk often. If you're a Transmuter, it's a given. With this, you can make sure you have aerial superiority or even force your foes to land. Swift Action blasting every round to stress the point is also pretty cool. This is an Evocation/Transmutation spell, so you need to be able to cast Evocation.
Flesh to Ice[sup]Frost[/sup] (:evillaugh) - Your first real SoD! Woohoo!
Greater Enlarge Person[sup]SpC[/sup] (:plotting - Essentially, this is Permanent Enlarge Person. If you have a BSF, this is certainly handy, saving you the actions on buffing him (it?).
Lightning Leap[sup]CM[/sup] (:plotting - Transmutation doesn't usually move you around. Sure, it gives you the means to do so, but it rarely does so directly. This is rather unique, and damaging those in your path is rather stylish. Sculpt this for better maneuverability.
Heart of Fire[sup]CM[/sup] (:plotting - It doesn't stack with Haste, but Fire Resistance all day long, an OOC speed boost and the Fire Shield are all nice. Not to mention the combo with the other Heart of... spells.
Airy Water[sup]Storm[/sup] (:plotting - This is like Water Breathing, except it's actually good and has a decent duration. It lets your party fight better underwater, too.
Zone of Peace[sup]City[/sup] (:plotting - It's an Emanation around you preventing BSFers from drawing their weapons. That's pretty cool.
Trait Removal[sup]SK[/sup] (:thumbsup - If you can somehow trap Pun-Pun for a while, this is how you disable him. It also has plenty of use in removing bad racial traits like Light Blindless, weakening Bound Pit Fiends, and if you can cast it as a Full Round action with Uncanny Forethought (hasn't seen Errata yet...), you can use it mid-combat to remove annoying abilities.
Transmute Rock to Mud (:thumbsup - Utility is awesome, but entrapping foes with this followed by TMtR is even better.
Transmute Mud to Rock (:thumbsup - A really good spell in a swamp, and with TRtM it's even better.
Overland Flight / Draconic Flight[sup]Draconomicon[/sup] ( / ) - If you plan to use this indoors, get one of the spells that improves maneuverability or the Pectoral of Maneuverability. Otherwise, this is your first hour/level flight spell. DF is an odd spell, since it's just a faster version at the same level (?!).
Greater Blink[sup]SpC[/sup] (:thumbsup - I don't like wasting actions on defense while in combat, but this is pretty good, I admit. With Eyes of the Oracle active, this offers immunity to most things.
Xorn Movement[sup]SpC[/sup] (*) - Because Earth Glide is just dandy!
Swift Etherealness[sup]PHB2[/sup] (*) - When you need it, you really do. Still, this is a 5th level spell!
Form of the Threefold Beast[sup]PHB2[/sup] (:turkey - Probably the worst combat form spell for it's level. If I'm losing my casting for the duration, I'm expecting something good.
Mental Pinnacle[sup]SRD/XPH[/sup] (:evillaugh) - Become a powerful Psion for the encounter! Cast this spell once and you'll last the encounter. Ask your DM whether you get bonus PP for a high INT score - I'd rule that yes. An Enchanter casting this spell can manifest powers with a truly scary DC.
Brilliant Blade[sup]SpC[/sup] (:evillaugh) - Truly a good spell when meeting anyone wearing armor or using Arcane spells.
Lesser Dragonshape[sup]DrM[/sup] (:plotting - None too shabby. You can rip a level appropriate foe apart, especially if you're pre-buffed.
Scalding Mud[sup]Sand[/sup] (:thumbsup - This is like Stone=>Mud=>Stone, except they take damage, and it's just one spell. Not bad, I think, especially combined with Solid Fog or somesuch.
Flesh to Stone (:thumbsup - It's a Save-or-Die. I actually like those, even if I often prefer stuff like Slow or Black Tentacles. Even so, unless you can use Flesh to Ice, this is the earliest you get a real SoD.
Disintegrate (*) - This is an old staple, and quite a bit overrated. Damage is good, but only if they fail their save. A level earlier you got a Save-or-Die, so this don't impressin' me much. The utility of this spell is very good, with destroying walls, floors, Walls of Force and the like, though. If you want this kind of damage, without a horrid save, look at Stored Lightning Bolt (SoS).
Mage’s Lucubration (*) - Think of it as a Pearl of Power 1-5 for a 6th level spell. Not bad, but not the best use for the slot.
Ooze Puppet[sup]SpC[/sup] (:thumbsdow) - Not something I'd prepare, ever, unless I plan to meet an Ooze. But if you do, it's truly good. My very own Living Spell? Sign me up!
Tenser's Transformation (:turkey - I'm now a Fighter! Except I'm scrawny, have no proper equipment, and far more stupid than a wizard or fighter should ever be. This should be [Mind-Affecting, Stupid].
Nightstalker's Transformation[sup]SpC[/sup] (:turkey - This is like Tenser's Transformation, except you at least get Evasion and SA. This MIGHT be good if you cast it along with using Shapechange/Polymorph, but it's still a terrible spell.
Elemental Body[sup]SpC[/sup] (:evillaugh) - Immunity to Stun, Parlysis, Poison, Sleep... the list goes on and on! Oh, and you can Fly (Perfect) at your base speed all day long. This is my favourite Transmutation spell!
Glass Strike[sup]SpC[/sup] (:evillaugh) - This is a Fort save or die... that affects Objects! You know what that means, right? Use it on Undead and Constructs while laughing like mad!
Reverse Gravity (:evillaugh) - Assuming they can't fly, this isn't a Save-or-Die; It's just a Die.
Statue (:evillaugh) - Hardness 8 all day long is fun. Not only does this reduce damage by a lot, it also cuts energy damage down by quite a bit. This is even better on your allies.
Control Weather (:plotting - Hurricanes are fun, and you can decimate whole armies with this. Takes time, but it's worth it.
Brilliant Aura[sup]SpC[/sup] (:plotting - Personally, I prefer the other options and using Brilliant Weapon, since not all your allies need it, but I can't say this is bad. Your entire party ignores Armor and Shield bonuses.
Unicorn Heart[sup]CM[/sup] (:thumbsup - That's no flight, but the bonuses to skills, increased speed and DD are useful. Along with Elemental Body or the other Unicorn... spells, this is rather nice, but still, we're talking 7th level spells here...
Body of War[sup]SpC[/sup] (:thumbsup - So I get to turn into a mighty Warforged Titan! Wow! You can't cast spells now. Congratulations, you're a BSF, but at least you're an OK one. The amount of immunities this gives is HUGE, and even though you have no CON score, you keep your HP.
Synostodweomer[sup]SpC[/sup] (*) - Whoever said Wizards can't heal, obviously missed this spell. Hardly efficient, but when you need it, you really do.
As the Frost[sup]PHB2[/sup] (*) - Not the most powerful spell, but Slow is good. Useful vs. very mobile foes who are smart and want to kill you specifically, and the DR is not bad at 10/Magic and Piercing. It also makes you an Outsider with Cold Immunity for the duration.
Adamantine Wings[sup]CM[/sup] (:thumbsdow) - You can get almost the same effect with lesser spells. Still, this one offers some utility in letting you bash down doors and getting a Quickened Blast for free.
Polymorph Any Object (evillaugh:evillaugh) - Turn your allies into Sun Giants! Turn your foes into Rocks! Utility abounds! If you don't use it as a buff, it's not actually broken, just really good.
Greater Celerity[sup]PHB2[/sup] (*) - Unless you have some sort of reason to use a Full Round Action, such as Uncanny Forethought or a Full Round Action spell, I really don't see how this is worth 4 (!) spell levels above Celerity. Even so, I can't discount it totally, since it has SOME use.
Ghostform[sup]SpC[/sup] (:thumbsdow) - If you're a Sorcerer, this is much more interesting. Anyhow, it's a useful spell to know, but you don't really want to waste an action casting it. Also, it's only a slightly improved, if at all, version of Greater Blink (SpC)...
Shapechange (evillaugh:evillaugh) - Turn into whatever monster you like and abuse any racial trait! That's the pinnacle of transformative magic, and is every bit as broken as the lesser versions. By now, you've come to expect this.
Time Stop (:evillaugh) - You'd just stopped time. That's quite a feat, right there! Relish it by using Rainbow Falls and casting 3d4 Stored Lightning Bolts for ~1050 points of damage.
Replicate Casting[sup]SpC[/sup] (:plotting - Not quite Time Stop, but if you want to cast Heal, a prohibited spell, or even follow a Planeshifter, you need this.
Dragonshape[sup]DrM[/sup] (:plotting - You don't generally want to enter melee, but with this you might just beat them in their own game.
Planar Perinarch[sup]PlH[/sup] (:thumbsup - Interesting spell. This lets you literally be God, after a fashion, on many planes. Don't expect the local powers to appreciate your messing around with their domain, though. Were this usable on the Prime, I'd rate it higher.
Transmute Rock to Lava[sup]SpC[/sup] (:turkey - You don't use 9th level spells to deal paltry damage, especially if it's Fire damage.