Ho-oh is pretty cool to use, the only reason it is not used, is that SR really hinders it by taking away 50% of its health on the switch-in. Lets not forget SR is the most used move. :\
Manaphy is nice with the 100 base stats everywhere, Water STAB is great too, and Hydration is an awesome Ability. Surf is usually better than Hydro Pump in most cases due to higher accuracy, but some Pokémon like Starmie need Hydro Pump's power to nag some OHKOs (Scizor and such can be OHKO by Hydro Pump (with SR), but Surf cannot).
Well, stuff like Darkrai, Mewtwo, Lugia, Rayquaza, Kyogre, etc is definitely Uber, but Ho-oh, Manaphy, Lati twins (without Soul Dew), is the most underused Ubers.