Tornadus / Tornadus-T: Good SAtk and STAB Hurricane, which never misses in the rain.
Thundurus-T: Massive SAtk and STAB Thunder, which never misses in the rain.
Jirachi: Good SAtk that can be boosted with Calm Mind, and gets Thunder.
Genesect: Great SAtk, and gets Thunder and get utilize Hidden Power [Water].
Dragonite: Good SAtk, can abuse Thunder, STAB Hurricane, and Rain boosted Surf. Can run a mixed set with Outrage.
Gyarados: Great Atk and can boost with Dragon Dance, and abuse STAB rain boosted Waterfall and abuse Moxie, turning it into a deadly Physical sweeper. It can abuse Thunder too! Just kidding. Don't abuse Thunder on Gyarados.
Gengar: While normally not a weather sweeper, it can utliize Thunder and Hex together quite nicely.
Jellicent: Also, not normally a Rain sweeper, but STAB Water Spout will hurt if it has full health. Slap a Choice Scarf to remedy the Speed.
Jolteon: Abuses Thunder and can take Electric moves for Rain teams.
Vaporeon: Normally used as a wall, Life Orb Hydro Pump or Surf coming from 110 base SAtk stat will hurt. Also can boost with Work Up.
Rotom-W: Abuses STAB Thunder and Hydro Pump, which are helped by the rain.
Toxicroak: Boosts with Bulk Up and Swords Dance, and heals itself with Dry Skin.
Tentacruel: Often used as a Special wall, it can use a Life Orb set of Giga Drain, Sludge Wave, Hydro Pump, Ice Beam is usable in the rain. Rain Dish will cover for Life Orb recoil.
Latios: Latios gets Surf and Thunder in the rain. Choice Specs is a big threat to lots of teams.
Volcarona: This fiery moth gets Hurricane, easily abused on a Quiver Dance set with it's monstrous SAtk stat.
Starmie: Starmie gets STAB Surf and Hydro Pump, as well as Thunder. It can also spin hazards that trouble rain teams. It can run a Specs or Scarf set with Trick.
Keldeo / Keldeo-R: Keldeo gets an insanely powerful Surf / Hydro Pump in the rain, and can boost with Calm Mind. It gets good coverage with Secret Sword.
Magnezone: It can abuse Thunder, as well as trapping Steels and setting up Charge beams on then behind Substitute.
Toxicroak: Can set up in the rain with Swords Dance and Bulk Up, gaining great recovery with Dry Skin and Black Sludge.
Cloyster: With Shell Smash and Skill Link, it can easily break through teams with STAB Icicle Spear and Rock Blast, as well as STAB Razor Shell.
Azumarill: Huge Power and Choice Band gives Azumarill 600+ Attack, and has rain boosted priority Aqua Jet, as well as Waterfall.
Empoleon: Usually a Special wall, it can use Agility to boost its Speed and abuse STAB Hydro Pump or Surf with its base 111 SAtk.
Froslass: Froslass gets a 200 base Water Weather Ball in the rain, turning it into a decent special rain sweeper.
Roserade: Also receives Weather Ball, and has Giga Drain and HP Ice to cover Pokemon that resist Weather Ball.
Kingdra: Has Swift Swim, and can go both Physical and Special. Usually used as a Dragon Dancer with Outrage and Waterfall, a combo only Shedinja and Empolen resist (I believe), or Choice Banded / Specs.
Raikou: Raikou also received Weather Ball and has Thunder.
Porygon-Z: Massive SAtk, and you will have trouble if it gets a boost and SAtk. It has Thunder to be abused, and also can have Adaptability Tri Attack, which hits ridiculously hard.
Sharpedo: Has great attack and boosts it's Speed via Speed boost, and can go mixed. Life Orb STAB Waterfall in the rain will hurt.
Zapdos: Has Thunder. Should've gotten Hurricane, IMO.
Nidoking / Nidoqueen: Gets Life Orb Sheer Force boosted Thunder, and will seriously hurt if unprepared.