My game uses a modified Gestalt system, in which Prestige Classes are not allowed, but the abilities are available to be taken as feats. The other major change is the combining Hide with Move Silently and Spot with Listen. This campaign uses the spell point system, where after each fight, each character regains SP up to 75% of the maximum after the first fight, the cap reducing by 25% every time that you fall below the threshold.
How I made my characters gestalt is by having them be touched by a deity that had come to the Material Plane to escape the entity that was stealing their power. This has happened all over the realms, and the deities chose seemingly random people to bestow their abilities on (Think Helm walking past his temple's weapon master to bestow his gift on a fresh, unbloodied recruit...). As a result of this, even the most organized of religions fell into varying levels of anarchy and schisms in nearly every faith-group.