Manaphy- Controversial and might need testing if you want to drop this down, but if kyogre is somehow allowed with manaphy, then forget it.
Mew- I would actually lean this towards the ubers side not exactly because of its unpredictability, but more of the things it can do effectively (ex. trick, explosion, transform)
Ho-oh- Imo it should stay uber. One of its weaknesses is rock, but a good amount of rock attackers are slow and weak to earthquake (that and those weird sub + recover ho-ohs will just wait until stone edge misses or runs out of pp). Water for the most part are special attacks, and after a single calm mind, ho-oh will laugh at any water attack. There is stealth rock, but ho-oh can instantly recover that off and still have plenty of hp to survive thanks to its mega special defense and good defense.
Palkia- This is an uber. Palkias that carry rain dance or something that uses rain dance with damp rock usually mean there is no counter to this.
Dialga- This is an uber. I'll cut to the point on dialga using one of its common movesets. Bulk up/dragon claw/rest/sleep talk is almost unbeatable in ou. Even if you do roar it away, it'll eventually come down to the last pokemon, and you won't be able to stop it. You're going to need some hard special hitter like a speced gengar's focus blast to have some chance of bringing dialga down.
Darkrai- Imo darkrai isn't as bad as he sounds, but I would still stick him up in the ubers section for now. The mixed version is what really worries me about darkrai being in ou.
Deoxys-D- I'm leaning this towards ou. A lot of people say that deoxys-d has that infamous spike/recovery move/taunt combo, but so does skarm. Deoxys's weakness is similar to cresselia's, so I don't see why not try this out. The only thing I would caution about is its ability to calm mind/cosmic power.
Kyogre- This is an uber. I would not be happy knowing that a monster that can shoot out a 150 bp water move in the rain will be raping half of my team.
Wobbuffet- Just test this one.
Lugia- Uber. The only two ways I can think of that can reliably stop lugia are: gengar and toxic. I am not going to use gengar just because of lugia, and toxic wars won't even work half the time on lugia if its user knows what he's doing. Lugia has mega hp and good speed. That means it can sub/recover/reflect/whirlwind without much of a problem. Aka, lugia can avoid status inflictions and still wall perfectly. I guess weavile can do the trick, but it would need to get in there before reflect goes up.
Also, something was bothering me for some time. Isn't dragonite just as threatening as rayquaza? They're the same exact thing, except dragonite is slightly weaker...and that rayquaza has overheat while dragonite has fire punch.
Deoxys-D: Skarmory sure has that combo, but it dies on Thunder/bolt, flamethrower and Fire Blast. Deoxys-D, however, has both MONSTROUS Defense AND Special Defense. It's only a slower version of Lugia. Not to mention it can Light Screen/Reflect as well. With Taunt + Cosmic Power... Try that thing... You can barely touch it. Give it Toxic, Taunt, Cosmic Power and Recover can kill off any team without Aromatherapy. Even if one team DOES have Aromatherapy, once that therapist is fainted, your team is prone to toxic again. Steel/Poison types, Magic Guard and Immunity and Poison Healers are exception, but they can be taken down by another member. Deoxys-D covers the rest.
Darkrai: Yanmega, Hitmontop and Ninjask and Aerodactyl say hi. You can take a Focus Punch Gengar, you can take a Tyraniboah. You can have Yanmega or Crobat's Hypnosis... Now Darkrai's to be banned.
Rayquaza: I do agree that it's just a better version of Dragonite.
Mew: The Pokemon of ALL MOVES... I'm not going to put up with that in OU. It's too almighty.
Kyogre: Uber if its counter, Groudon is not being brought down, but I'd consider it Uber anyday. It's only to be walled really by Shedinja and Giratina, and that's only the standard set. If the Kyogre has Aqua Tail & Thunder Wave, it can be extremely dangerous!
Ho-Oh: Things like Aerodactyl can kill it with easy. Rock Slide or Stone Edge STAB on Aerodactyl deals an ENORMOUS amount of damage on Ho-Oh's 4x-weakness. Gyarados' Aqua Tail and Intimidate eats it quite badly, just carry a Rawst/Lum Berry if you are afraid of a burn. You can also have a Modest Persian Hypnosis, Nasty Plot and Power Gem. Starmie's Power Gem also deals an enormous amount of damage, but since it usually don't carry that, then STAB Surf would have to do. It has recover and can switch into Sacred Fire as well as shake off the Burn with a simple switch. ScarfCross and ScarfChomp are also able to Stone Edge this thing pretty easily, but becareful of ScarfCross' miss on Stone Edge... Scarf-Oh can be a problem, but Heatran/Houndoom takes the Sacred Fires anyday, and Earthquake can be solved by all Levitaters and as well as Flying types. This thing worths a test.
Lugia: Same with Deoxys-D... Quite ubersome. It's too defense, plus it has Whiriwind, Calm Mind and Recover/Roost.