I'll post my "Ratmann gets the sad ending" theory here. Minor portal 2 spoilers, that have already been released, for you wussies.
Basically, It's already been announced that you'll see more of Rattman's murals; specifically showing your defeat of glados. I recall seeing a screenshot (i cant find it, sadly) that showed, in a ruined test chamber, the portal gun, and a MASSIVE one, all across one wall. My theory goes:
Rattmann survives the shot. Maybe the relaxation vault heals him; maybe he simply survives. The vault carries him and the cube back down into the first few test chambers. These are now ruined, of course. Rattmann wanders through the chambers, leaving his drawings along the way. He's now out of medication, so expect him to become more and more raving and church-guy-ish. These drawings in the first few chambers- i.e. the start of the game- will serve as exposition for Mrs E Culucket in Moose Springs, Pensylvania, the one person on earth who hasnt played Portal 1 yet.
Rattmann will be long dead by portal 2. A crazed man with a cube wont last long in the test chambers. Lack of food, or water, or exposure will get him. He'll fall, or commit suicide. Poor bugger wont last two months. I really hope this happens; i like him, but to gie him any other ending would be ...artistically wrong. He needs a sad ending, he's a tragic character.
I really hope we dont find anything of him. A face-to-face meeting would be unbelievably crass. Discovering remains less so but still... dissapointing.