Kyogre - It certainly gains originality points. While it is nice to see a kyogre that isn't choiced, you might want to switch Aqua Ring with either Calm Mind, or run a Specs/Scarf set and run HP Fire to deal with the Ferro walls that run around. Other than that, it seems pretty solid.
Rayquaza - Nothing to say. Pretty standard set, covers most threats in Ubers. Not much you can do to it will make it better.
Arceus - Good Arceus. I agree that you should get Shadow Claw as your 4th move, because you would get walled by seriously ANY ghost type, not just Giratina.
Lugia - Your EVs do not support the moves you use. Either get a non-offensive move or get special atk investment over Def/Sp.Def. If you change your EVs and/or moves that can be a very good lugia set.
~~~~~Edit 1 - Might want to drop Psychic to run both Thunder and Hydro Pump. Just because it's STAB doesn't make it the best choice. Psychic can't really hit most of Ubers super-effectively, since it is only effective against Poison and Fighting.
Giratina - WoW and D-tail are good. keep those. However, I recommend dropping T-wave for either Draco Meteor or Shadow Sneak. Draco Meteor is powerful whereas Shadow Sneak can be a very reliable form of priority. Rest isn't really good or bad, if you use it right it can be very good.
Shaymin-S - Your 3 moves are standard, and Aromatherapy is good for waking up Giratina to wall more stuff. If you play it right that can be a potentially game-changing combination.