I'll start with Manaphy. He's pretty cool. I use him a lot in Ubers, the reason being its ability, Hydration. If it's paired with Kyogre, it basically removes its status problems. The trouble is, Rest is its only recovery move; if your opponent sends in something like Tyranitar as you Rest, you're pretty much screwed until you send Kyogre back in. But if you can take care of opposing weather inducers and let Manaphy set up, your opponent is in for a torrent of trouble.
The Prince of the Sea (Calm Mind)
Manaphy @Leftovers
Ability: Hydration
252 HP, 252 SpAtk, 4 Spe
Modest Nature (-SpAtk, +SpA)
Calm Mind
Rest
Surf/Scald
Ice Beam/Grass Knot
Calm Mind is the crux of the set. It boosts the little water pixie's SpAtk and SpDef by one, so it can stay on the "bulky" side while it retains its power. Rest is there because of its ability, Hydration, which allows it to heal any status on the first turn in the rain, so if Manaphy's HP dwindles, you can Rest off with no restraint. It also makes things like Thunder Wave or Dark Void useless, so it can be an effective absorber against Darkrai. Surf is for more power, but Scald has that 30% burn rate, which is always helpful. The last move depends on what your team needs, but either way, something walls you. Ice Beam hits Dragons like Rayquaza and others like Groudon, but leaves you walled by other Kyogre. Grass Knot takes care of Kyogre and still hits Groudon hard, but leaves you walled by most Dragon-types.
Battleship (Tail Glow)
Ability: Hydration
Manaphy @Life Orb/Leftovers
4 HP, 252 SpAtk, 252 Spe
Timid Nature (-Atk, +Spe)
Tail Glow
Rest
Surf
Ice Beam/Grass Knot
This is a much more offensive Manaphy. This time, you replace Calm Mind with Tail Glow, a move that increases SpAtk to +3! With Life Orb equipped, if can do some heavy damage. Here are some damage calculations to show off its power.
+3 252 SpA Life Orb Manaphy Surf vs. 4 HP / 252+ SpD Eviolite Chansey in rain: 294-347 (45.79 - 54.04%) -- 46.88% chance to 2HKO
+3 252 SpA Life Orb Manaphy Surf vs. 4 HP / 252+ SpD Blissey in rain: 368-434 (56.44 - 66.56%) -- guaranteed 2HKO
+3 252 SpA Manaphy Surf vs. +1 204 HP / 0 SpD Mewtwo in rain: 352-415 (87.12 - 102.72%) -- 18.75% chance to OHKO
+3 252 SpA Manaphy Surf vs. 252 HP / 0 SpD Groudon in sun: 350-414 (86.63 - 102.47%) -- 18.75% chance to OHKO
+3 252 SpA Manaphy Surf vs. 252 HP / 180+ SpD Tyranitar in sand: 330-390 (81.68 - 96.53%) -- guaranteed 2HKO
+3 252 SpA Manaphy Surf vs. +1 252 HP / 0 SpD Lugia in rain: 222-262 (53.36 - 62.98%) -- guaranteed 2HKO
Whew, that's some power! Anyways, again, the moves in the last slot are completely up to you.
Other Options
Hidden Power, Choice, U-turn
Checks and Counters
Choice Scarfers like Zekrom, Palkia, and Dialga can outspeed and kill it with a Thunder. They won't do much to the Calm Mind set after +1, however. Calm Mind Arceus-Electric is also a good counter, which can Calm Mind alongside Manaphy and OHKO the Tail Glow set with Thunder. Taking away the rain helps, too. Groudon and Tyranitar are shaky checks, but they remove Manaphy's rain. Choice Scarf Kyogre is a good counter, as it can come in and revenge kill it, but Kyogre can't take a Grass Knot. Rayquaza, although it is KO'ed by Ice Beam, can come in on a predicted Rest and proceed to set up.
Now for Phione, Manaphy's little brother. It doesn't seem too bad at first, sitting at base 80 in every stat. Of course, they aren't huge, but it looks enough. So why is it sitting at the bottom of NU? Its movepool is terrible, and it doesn't even get Calm Mind! What it does best, however, is setting up rain for its teammates.
In the Shadow of the Storm
Phione @Damp Rock
Ability: Hydration
252 HP, 252 Def, 4 Spe
Bold Nature (-Atk, +Def)
Rain Dance
U-turn
Rest
Scald/Toxic
This is Phione's best set. It can set up Rain Dance for sweepers like Gorebyss, and get out of a sticky situation with U-turn. Scald is so you don't become Taunt bait. However, Toxic is viable as well.
Other Options
Life Orb, Safeguard
Checks and Counters
If you can KO Phione before it sets up rain, you have basically countered Phione. Fast Electric types like Raichu can do the job. Pokemon with Taunt can easily stop Phione as well.
Opinion: Water is my favorite element, so naturally I would like both of them. I prefer Manaphy, however, probably because it possesses more of an offensive presence.
Prediction for next week: Genesect