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 Well, of course the first thing that pops to mind concerning amnesia and Eberron would be the Daelkyr or whatever they're called, the abominations.
 I just watched Inception the other day, so maybe you could borrow a bit from the plot of that movie - your character is a freelance spy, working for one of the five governments, that was contracted to steal memories of some kind of secrets having to do with the War from some former intelligence officer or perhaps a rich merchant... Let's say the character was told the "secret" was the schematics of some uberweapon (possibly the cause of the destruction of Cyre?), the location of a previously unknown huge stash of advanced warforged prototypes or maybe even a Creation Forge. When the character and his team track down the target, they find they've stumbled onto something much larger than what they thought was going on - while rummaging around in the guy's head (represented in the target's mind by the physical locations where his memories took place), the rogue breaks into a locked place and opens a particular door only to discover that, instead of 50-yr-old state secrets, he's stumbled into a wide-reaching mind-flayer conspiracy...
(The target was secretly a double-agent working within his government's intelligence network in order to facilitate the workings of his true masters, based in Xoriat.)
 Having tripped some sort of psionically-implanted mental alarm or trap in the target's mind, a psychic backlash was created. Designed to pretty much blow the top of the rogue's head off, the rogue barely avoided it or somehow turned it around, resulting in the target's death from brainfry and the rogue having his memory wiped.
 Although the conspiracy would be surprised as hell to find out that the rogue is still alive, the rogue is just collateral damage and of no great concern to them. However... Unknown to both the rogue and the conspiracy, the rogue (always looking to make a bit more profit) also pilfered some other information during the mission that may or may not be related to the conspiracy, but which is of immense importance. What that information might be or what form it may take is probably best left up to the DM and wherever he wants to go with it.
On a related note, perhaps the government of whichever nation the rogue's target was working for is still looking for the rogue in connection to the murder of the target, who obviously would have been somebody important and powerful. Since the rogue doesn't know who the target was or which nation they were from, there may come a day when the rogue comes across a wanted poster or is otherwise informed that there's a reward for information on and a warrant for the arrest of someone who looks suspiciously like the rogue...
 The rogue may or may not be haunted by half-remembered dreams or flashes of images from his previous life, particularly the brief image of him being before a door with an immense sense of dread as his hand reaches for the knob, or perhaps no matter how hard he tries the image ends before he can open it and thus remember what's on the other side.
Perhaps the rogue also has some object (which he knows is important, but can't remember why or where he acquired it) that might have some connection to him losing his memory. (Or perhaps it's only important to him because it has sentimental value - perhaps the amnesiac rogue left somebody he cares for behind when he wandered off with his memory gone...)

 Alternately, if you want to turn that around and invert it, perhaps the character might eventually find out that they were part of a failed Daelkyr plot, and that whatever caused the plot to fail wiped their mind.. (And may have even completely rearranged their personality, as well - they could have been a seriously depraved villain up to that point. As the character's a rogue, maybe they were employed as an assassin before they got their egg scrambled?)