i am currently running the Shackled City AP with 3 players. We started with 2 and so I had each player play 2 characters. The natural progression was that one of the PCs became more of the speaker and the other the strong silent type (works out well for the characters backstories). For example, one player is a Paladin of Heironeous. His second character is a Goliath Barbarian with low self esteem who isn't really comfortable around humans other than the paladin. So most of the time he just follows his lead anyways. The other player is a Gnome Wizard and some sort of planetouched Ranger (like trumpet archon) who can't control the volume of his voice and looks real freaky too. Again, one of the characters ends up doing a lot of the roleplaying (in this case, the gnome.)
The great thing about this situation is the increased use of tactics and also a sense of comraderie among the characters that is the result of being effectively controled by the same person.
The unfortunate thing about this, is that the individuals PCs characters rarely get to interact with one another and when they do, its slightly disturbing to watch a player talking to himself.
During character creation, i tried to make the PCs pick 2 classes that wouldn't have too much of a personality conflict though. Like I wouldn't have allowed the Paladin to also play a rouge (just too many missed roleplaying oppurtunities.) I would highly recomend this. Don't have an evil wizard paired with a cleric and for that matter it's best to have one spellcaster per PC.
The third player was brought in a little later so they are only playing one PC (the rouge). This also works out well because the player is new to 3.5 But, if all goes well, he may be playing the party cleric as well (prolly a neutral one.)