The PCs in my campaign have taken levels in arcane archer, archmage, deepwood sniper, green star adept, incantatrix, loremaster, order of the bow initiate, and stonelord.
As a player, I have levels in dervish and a homebrewed prestige class (blademaster).
As a DM, I frequently use weapon masters (my all time favorite prestige class). Off the top of my head, I've also used archmage, frenzied berserker (without the extra Power Attack damage boosts), war hulk, hulking hurler, alienist, argent savant, assassin, lasher, master of chains, battlerager, fiend of corruption, knight of the chalice, orc blademaster, spellfire channeler, spellfire hierophant, pious templar, and runescarred berserker. I'm sure I've used quite a few more.
I find my favorite prestige classes to be the most generic ones, those that simply help round out a niche rather than try to exemplify an organization. That's why my list is skewed mostly towards older prestige classes (or those that have been updated from older sources).
I can't think of any prestige classes I've outright banned, but I won't allow any ability that increases Power Attack beyond the already overpowered 2-for-1 with a 2-handed weapon.
I consider new prestige classes to be of little value in new source books. The new format is so bloated that the opportunity cost just doesn't make them worthwhile. Add to that the fact that most of the newer ones tend to be more tied to organizations than expanding a role, and I've mostly lost interest in them. I do like to see prestige classes for the new core classes that have little support, like the recent warlock prestige classes.