The harder question for me is which classes would I ever consider allowing in my game.
The answer to that is pretty much only those classes which facillitate other wise difficult multi-classing combinations. The only really difficult multi-classing involves spell casting classes (particularly arcane spellcasting classes), and so the only PrC's which I would ever consider allowing from that list are Arcane Trickster, Eldritch Knight, and Mystic Theurge. Those are to me the easiest sort of PrC to justify. They do something useful and they do it in a fairly generic manner that is easy to paint as needed and fit into a game world. A clr5/wiz5/mystic theurge10 seems to me to be about as powerful as a clr20 or wiz20, and a clr10/wiz10 is most certainly not. Similar reasoning applies to combinations like rog5/wiz5/arcane trickster10 and ftr4/wiz6/Elderitch Knight10, because access to higher level spells is simply so powerful.
The other ones bother me for various reasons. Shadowdancer is about the best of them, because it is something like being able to take an alternative balanced 'rogue' class for levels 11-20. The thing that kills it for me is that its utterly front ended, to the point of something like Rog19/Shadow Dancer1 being rather attractive. The rest of them seem like straight forward 'base class only better' to me, and succeed at that to one extent or the other (Dwarven Defender and Heriophant being examples of not succeeding in it). Prestige class fighter and 'arcane caster' variations in particular annoy me, because Fighter is such a versital class as it is and has so little to lose in most cases by sampling from any class with full fighter BAB progression. Likewise, so long as an 'arcane caster' can keep his spell progression, he's got almost nothing to lose by sampling from any class that gives full spell progression because the SRD 'arcane caster' classes wizard/sorcerer have almost nothing going for them but thier spells. So where is the real trade off if you can take 10 levels of something and get 5 or more feat equivalent abilities out of it plus not lose anything from your spell progression?
I honestly think that the worst of them is Blackguard, because it is a bad fix to the badly designed Paladin class. To see an example of Paladin/Blackguard done right, see Green Ronin's Holy Warrior/Unholy Warrior. Dragon Disciple is cheesy, but on top of that its another example of a class which seems to suffer from much better mechanical solutions existing, for example the racial levels in Savage Species or AU.