Gestalt... Experimenting Still
I've been playing Gestalt since shortly after Unearthed Arcana came out. Obviously, there are not many rules for Gestalt, so most of it you end up having to make up as you go. There is nothing for it but playtesting.
We have been using the following system with great success. If a race has a level cost, it counts for half of your "level". However, you also have to increase the cost of races. For example, in our campaign a half-celestial template costs 8 levels. An 8th-level character could be a half-celestial dwarf with 8 fighter levels or a normal dwarf with 8 fighter levels and 8 ranger levels.
The biggest change we've had to make is to saving throws. With being able to multiclass like crazy, saving throws "broke" very quickly. Before long, nothing could fail a save. Now, we have all PCs, NPCs and monsters choose two "good" saves and one "bad" save regardless of classes. Thus, every single creature or character with 15 Hit Dice has two saves at +9 and one at +5. Without this change, spellcasters were useless because saving throw spells were resisted unless someone rolled a "1".
We've found gestalt characters to be stunningly powerful, but a heck of a lot of fun to play. In general, we've found that ECLs should be anywhere from 2 to 4 levels higher for gestalt characters. Also, with half the party made up of clerics, we've set a limit of "9 lives" for every character. After 9 raisings, you cannot be resurrected from the dead by any means, including a wish.
Gestalt play has been very rewarding, and it allows players to experiment with much more complex, rich-storied characters as well as play with different classes and abilities that time would simply prevent them from doing before. For example, if you want to play a full power wizard and a rogue, gestalt lets you do both at once. Before, you had to wait until one character was removed from the game (death, etc.) before you could try the other. My players have absolutely loved it.
Charles Plemons