My group does it as both HD and LA apply to one side of your Gestalt. Its fine as long as the DM is wise with what Templates and Races he allows... as with any other D&D character.
Tiefling Fighter 1 | Rogue 2 (or Fi 19 | Rog 20): not going to break your game... (or, if it does... your game is weak anyways!

)
Elf Shade Vampire Half-dragon Rogue 5 | Sorcerer 20: Eh, it might. Might not. YMMV.
Our current Gestalt party:
Raele: Lycanthropic Ranger something, not sure of his exact build, the player is rather secretive, and I'm not DM.
Anixiel (Nixie): Faen Lorespryte 1/2 Black Dragon Rogue 2 (?) | Telepath 5. Our own tiny pseudo dragon. Schticks: Flies around and spits acid... or fire... or electricity or soundwaves... (most of his psi-powers are described as breath weapon. Energy Missile, Energy Retort, Mind Thrust, etc). Will once in awhile catch the opponent with a blast of fire in the face (Energy Ray + Sneak attack).
Onslaught, aka Legion (mine): Warforged Barbarian 1 / Fighter 4 | Psion-shaper 5. Is one tough nut to crack, but has been in the negatives at least 3 times. Primary schticks: being tough (Vigor, Sharepain, etc), and summoning "ghostly" (coughectoplasmiccough) members of his lost legion... aka Astral Construct. Note the lack of a template, no HD or LA, still manages to be as powerful as the guys with LA and/or racial HD mixed into thier builds.