Ah, Manaphy. Somehow, the only BS-100 legendary currently Uber. I guess it's cause of Tail Glow, but seriously, I'll take Jirachi over this thing any day. Anyways, when looking at Manaphy, a few things stand out. One, besides Tail Glow, it completely and utterly lacks any defining characteristics that set it apart from any other bulky Water. Defensive sets are outclassed horribly by Vaporeon. Therefore, one must abuse his calling card, Tail Glow, in order to potentially get a sweep. While not the most effective thing in the world, I think a SubSalac set might be decent.
Manaphy @ Salac Berry
Timid - Hydration
252 Speed, 252 Sp. Atk, 4 HP
-Substitute / Rest / Hidden Power (Grass)
Problem is, Manaphy suffers from 4MS badly. It can't carry everything it needs to carry in order to effectively sweep. Without Substitute, it can't reliably activate Salac Berry. Without Rest, it's priority bait. Without HP Grass, Kyogre and friends wall him to hell and back. So, you've gotta pick and choose a bit.
All in all, I wouldn't recommend this thing. Just use Vaporeon or Kyogre. Or drop him to OU where maybe he can see some real use.