Let's see. In my current campaign I allow three non-standard "core classes" and a total of 12 PrCs, only two of which are from WotC sourcebooks. We also dropped some of the standard classes, such as Monk and Druid, as well as replacing the Paladin with the Green Ronin Holy Warrior class.
In my next game we will be using Arcana Unearthed as the base, but will add in 3 other "core classes"; PrCs are up in the air at the moment, but probably not too much from WotC.
I am pretty open that way, as long as the classes and the campain flavour mesh.