The best gestalt combos seem to involve a passive side that gives constant benefits and an active side, for powerful actions to take in combat, since you may have twice the classes, but still the same actions per round.
If you can multiclass like crazy, I don't even know what the most overpowered combo could be, I can just imagine it'd look like caster/ full progression prestige classes cherry pcked for benefits on one side; an ungodly mix of martial class dipping and prestige classing on the other. If the DM really has no sanity caps, try to go for dual progression casting prestige classes on each side of the gestalt, maybe.
For a more simple an effective power combo, I always liked the idea of Factotum//Wizard (or Psion). Huge intelligence synergy, medium BAB, d8 HD, good proficencies, 6 + int skill points with every skill ever printed as a class skill, full wizard casting, and the cream of the crop comes at level 8...when you can get extra standard actions.
Slightly more complex combo would be a charisma-based caster (like sorcerer) on one side, the other side dipping for the massive amount of "charisma to X" class features out there. Paladin and Marshal dips give charisma to saves and (the entire party's) initiative, for example.