I tend to be very liberal with what I'll allow in my campaign- the only things that I've ever actually banned are Frenzied Berserkers (after one of my PCs became one in a previous game, which resulted in some nasty player vs player with 2 pcs winding up dead) and evil characters (because I want to run a heroic game- in my latest campaign I've only allowed good characters).
In my latest campaign, I'm trying to regionalise a lot of stuff- from materials, items and spells to PrCs -so specific stuff is only available in certain areas or from certain groups, and almost any PrC has roleplaying requirements of one form or another. I'm also allowing only the spells from the PHB, FRCS and Magic of Faerun to be taken at level up, while new spells from other sources will be available to purchase on scrolls in specific areas. Some of the variant base classes are regional too, but if the PCs want to take them, I'll only require they spend some time in training with someone who has the class.
Other than that, I pretty much allow the players to do what they like PC-wise. To be honest, I've always had more problems caused by specific character concepts (lones wolves, non-combat characters and the like), than with anything from sourcebooks.
Ellie.