There's tones of good gestalt builds out there. Things to remember....
1) MAD is still the enemy. Make sure both classes work off the same set of ability scores, because, well, they'll need to.
2) Synergize class features. Barbarian//Wizard may sound awesome, but if you can't cast spells while raging then you rather lose out.
3) A few classes make famously good gestalts. Monks and Factotums are generally much improved by the gestalting process, as their class features bolster the class they're paired with.
4) A few classes are just famously good, and rock as much in Gestalt as ever (or even more, now that they can cover their weaknesses). Druids, Wizards, and Tome of Battle classes especially deserve a mention here.
Shortcut: Pick any two of Wizard, Warblade, and Factotum, based on your playstyle and preference. Gestalt them. Win.