For Mewtwo, I would try to give it an item that boosts Sp. Attack, because the nature really doesn't do much for it. Also maybe one of the gems or arceus plates.
Zekrom's got some awsome moves plus the stab, so I think you want an item that boosts Fly. And if you already have these pokemon, give it an item that goes against what its nature does(drops Sp. Attack)
Ohhh, Kyogre's tough. Just give it an item that boosts one of its attacks, because thanks to the nature, you got a + Sp. Defense, and there aren't many physical grass and electric moves.
Now for Groudon. Give it a Passho Berry because thanks to eruption grass' weakness is taken care of.
Kyurem: You've got 2 pretty good ice moves already, plus stab, so with an icicle plate or a NeverMeltIce, these attacks would be BEAST.
Finally, Rayquaza. You might want to give an item that takes back the impish Sp. Attack drop. But if you don't have this rayquaza yet, and this is just planning, I can't think of any ideas for items so just hope you don't a nature that drops Sp. Attack.
Hope this helps!:)
WHEW. That was long.