The options mentioned above are great.
I've been quite happy with my experiences dealing with Troll & Toad and Beholder the Bargains. They're both great places to get single D&D miniatures.
If you just need some inexpensive counters to represent monsters and you aren't very picky about scale, whether they are painted, accuracy, and that sort of thing, there are also some great, inexpensive options in 1/72 plastic - a scale and material traditionally used for military war-gaming. I've found myself mostly delighted by Caesar Miniatures' 1/72 fantasy miniatures line (review
): it doesn't take a lot of money to get dozens and dozens of Dwarves, Goblins, Orcs, Elves, and humans; they're a bit small compared to most fantasy miniatures, they're not painted, but they otherwise look the part and should work fine for NPCs. This looks like one of the best bargains for fantasy miniatures you could possibly hope for. Caesar and other 1/72 plastic miniature manufactures also produce historical wargaming miniatures that might come in handy, including a fantastic array of historical figures, castles, siege engines, ships, and that sort of thing.
Keep an eye on garage sales and that sort of thing, too. If you're lucky, you can snag some fantasy boardgames full of miniatures on the cheap... the classic, out-of-print HeroQuest
is probably one of the more famous fantasy boardgames full of decent miniatures, but it's certainly not the only one out there. Wizards of the Coast also produced some great board games recently that have a great selection of unpainted D&D Miniatures in them... "Legend of Drizzt", "Wrath of Ashardalon", and "Castle Ravenloft", together, should give you plenty of great, popular monsters to work with.
Paizo publishing recently partnered with Wizkids to produce a great line of pre-painted random plastic miniatures that look right at home among D&D Miniatures. I'm sure the singles market for those should be a great way to get common monsters and pc types at a lower price than out-of-print D&D minis would go for.
And, what I've seen of Reaper's unpainted plastics ("Bones") looks great, seems quite affordable, and definitely needs some gamer support to encourage Reaper to expand the line.