Hhm, let's see...
What about natures, first of all? And EVs? Oh well, I'm assuming this is in-game...
Zapdos - since this is in-game, I doubt you'll have HP Ice or Grass. If you can get the Zapdos from XD, give it Metal Sound. For your current Zapdos, lose Charge and get Thunder Wave (Emerald Move Tutor).
Dragonite - Fly makes me cry. Special Dragonite is ok, but he can do so much more...
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EV: Sp Att, Def/Sp Def
Nature: + Sp Att, - Speed
Dragon Claw/Focus Punch
Substitute
Ice Beam/Flamethrower/Thunderbolt
Ice Beam/Flamethrower/Thunderbolt
There's a whole world of things Dragonite can do. Flame Claw hurts everything for neutral damage at least, or you can sub-Punch Bolt Beam, which hurts everything except Shedinja. Or, if you like, you can Dragon Dance.
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EV: Att, Speed, minor Def/Sp Def
Nature: + Att, - Sp Att
Dragon Dance
Earthquake
Rock Slide
Double Edge/Return/Flamethower/Fire Blast
Salamence does this better, but it still can work for Dragonite. Fire moves say hi to the physical walls that will slow you down (Skarmory, Forretress).
Mewtwo - well, meh. I'd rather stick a couple of elemental moves to benefit that monster Sp Att. Go with Ice Beam, it works in uber battles against everything, and Thunder for Kyogre. It's gonna do far more damage than Shadow Ball, that's for sure. I'd also lose Recover as well for this set. EVs in Speed (although max isn't completely necessary, unless you want to tie with other Mewtwos) and Sp Att.
Ho-oh - meh again. Psychic isn't nearly as great for a non-psychic type. Sacred Fire is ok. I'd also give Ho-oh a physical attack as well to surprise low defence ubers like Mewtwo. Either way, Kyogre says hi. (although you did give Ho-oh Thunder which is a surprise). Wallop some EV into Sp Def as well as your attack stats.
Lugia - meh times three. Aeroblast ok, consider Whirlwind over Shadow Ball if you're playing with Deoxys-LG. (although most ubers are psychic types, so Shadow Ball can be a nice surprise). Spikes is godly in ubers, especially since lots of teams like using Shedinja. EV in Sp Def, Def and Sp Att.
Deoxys LG - since most ubers use special-based moves, Mirror Coat can be a nice surprise. However, you will need the Sp Def, so I'd advise against using MC. Actually this needs a big rework:
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EV: Def/Sp Def/HP
Nature: + Sp Def, - Att
Night Shade/Seismic Toss
Spikes
Recover
Toxic
Toxistall variety. I'm not completely up on the uber metagame, but most don't expect Toxic, especially as an alternative to someone expecting Spikes.