I think it would work better in pre-3e games. I've only done close to 2 characters in 3e games though.
Here's the tale:
One of my players (the one who was really into the rules and the roleplaying the most in a lot of ways - also the only one who was planning on DMing) got tired of his current PC. Problem was, that PC was rather important to the next couple of adventures (and the other players were interested in those events too). He had made another character up, with backstory and everything. So I decided, what the hell might as well introduce him. All in all it worked out pretty well, occaisonally I would 'take over' one of the two characters for a brief response (usually this was to convey world information.)
This was actually made easier by the fact that we'd had a PC who'd been with the group for a long time who'd been run by a few different players. Gaazt was a barbarian half-orc in it for the money, and other rewards that everyone seemed to like, when there was no player to run him, I did but left most of the combat stuff up to the group. Occasionally on of the players (playing another character) would get a great idea and say Gaatz does X and I'd just roll with it, cause it was usually awesome.
By far the most interesting "two-characters" per player was a more recent game. A Two-Headed character. Human Bard 4/ Fighter 4 with the Two-headed template from Savage species. (Barckstory was the character was originally a bit of a multiple personality disorder before being captured by a Mad Archwizard and experimented on.) The one head was sort of the 'default talker'. All I can say was pure awesome. There was one really cool moment when the Darryl got in an argument with Richard (the other head, their collective name was Darrick or Derek.) More cool was when the other PC's asked one head, then the next what they each thought.
