I'm using Gestalt rules in Pledge of Tyranny and it's great. The heroes feel like they're something beyond an ordinary adventurer, and I'm having fun devising Ritual-Bonded villains with really nasty Gestalt combinations (right now my favorite is the Mage class from Elements of Magic combined with Fighter or Monk, or Anima from the same book combined with... anything else. But especially Monk. Heh... I'm having too much fun with evil Monks... ).
I'm looking forward to trying an Illumian gestalt character sometime. With their ability to switch their primary spellcasting stat, I think they could make amazing buffers!
For the record, I also like the idea of gestalting with an NPC class. Then you could even allow multiclassing on the 'free class', while the NPC class is fixed for all eternity.