Mewtwo: Protean (more bulky deo-A), Deoxys (Psycho Boost), Lugia (same)
Ho-oh: Gale Wings, Speed Boost, Magic Guard
Lugia: QuiverPass (masq), Unaware, Magic Guard
Latios: Adaptability, Turboblaze, Lugia (psycho boost)
Groudon: Unaware, Poison Heal
Groudon-P: Ho-oh, Rayquaza/Victini
Kyurem-Black: Refrigerate
Kyurem-White: Refrigerate, Sheer Force, Sniper
Kyogre-P: Masquerain
Slaking: PH, Adaptability, Genesect (Download + Espeed + Explosion), tons of other shit
Regigigas: Same as above
Rayquaza: Gale Wings, Speed Boost, Multiscale, Aerilate, Itself
Deoxys-A: Protean, Sheer force
Deoxys-D: Don't use this
Deoxys-S: Omastar, Skarmory, Genesect, Moldy Hazards, Azelf (nasty plot psychic)
Dialga: Adaptability, Druddigon (Moldy hazard set similar to standard uber lead), Levitate??
Palkia: Adaptability, Primordial Sea, Sniper, Masquerain, Revenvest?
Giratina: PH, Unaware, Magic Bounce, all of cress' sets
Darkrai: Zoroark
Arceus: PH, Bulky sets not run by the other two normal types. Outspeeds them as well.
Zekrom: Charizard-Mega X
Reshiram: Desolate Lands, Sheer Force
Xerneas: Slurpuff, Magic Guard, Poison Heal, Pixilate
Yveltal: Honchkrow, Magic Bounce, Speed Boost
Salamence-Mega: Dragonite, Rayquaza, Espeed whatever the fuck you want :)
Kangaskhan-Mega: Slaking/Regi have more bulk, more speed, and can hold items. Don't bother with this.
Mawile-mega: Toxicroak, Hitmontop
Gengar-Mega: Illusion, Mew (dual stabs + nasty plot)
Keldeo: Outclassed by palkia
Archeops: Outclassed by a lot of things except rock head
Blaziken-Mega is still really good.