If you're looking to create a 'Standard Doubles' tournament, then I'd suggest starting with the following Pokémon banned:
Mewtwo, Lugia, Ho-Oh, Kyogre, Groudon, Rayquaza, Deoxys (All Formes), Dialga, Palkia, Giratina (All Formes), Darkrai, Arceus.
Personally, I'd ban Mew, Celebi, Jirachi, Manaphy, and Shaymin (All Formes).
Basically agreeing with Sixonesix. Though in the Flat Battle, Phione is banned on the basis of it being technically an Event Legend, when it's obvious it doesn't need to be. But since I highly doubt anyone would use it unless we created a Tier List and had an NU category, having it banned and just simulating the Local Wireless Flat Battles in HeartGold / SoulSilver seems like a good idea.
Item Clause would be something I'd employ as a standard rule for once. In Doubles, more items are generally useful, and not just useful, but often required. Items such as Lum Berry, Focus Sash, Sitrus Berry, Chesto Berry, any -type resist Berry, Life Orb, Choice Items etc are just so worthwhile, it's not as simple as slapping Leftovers on half of your Pokémon. Soul Dew should be banned, though.
The only other thing is allowing the battles to be level 100 instead of 50, but I don't think many people would be too fussed, and just stick to the general level 50 rule already used.
The final major decision is.. Do we take six Pokémon but only use four (like in Flat Battle and Battle Revolution Doubles matches), or do we go ahead and use all six?
In terms of strategies, you're looking at just general teams with good Pokémon (GoodStuffs), Rain Dance, and Trick Room as the three most prominent all-out strategies. After that, it's just about synergy and combo's using abilities, resistances, and set up, making use of Fake Out etc. Protect and Explosion as well.
Trick Room
Users: Dusknoir, Bronzong, Cresselia
Abusers: Smeargle, Metagross, Snorlax, Tyranitar, Machamp, Abomasnow, Lapras, Camerupt, Rhyperior
Rain Dance
Users: Jolteon, Electrode, Bronzong, Crobat, Zapdos, Azelf, any Water-type
Abusers: Ludicolo, Kingdra, Toxicroak, Qwilfish, most Water-types and all of the users of Rain Dance, really (Magnezone, Raikou etc are a good shout as well)
GoodStuffs
Blissey, Breloom, Empoleon, Garchomp, Gengar, Infernape, Suicune, Togekiss, Salamence.. And basically everything listed above already.
I don't think there's much else that you could consider top tier, bar a few such as Hail abusers and Sun abusers, maybe some other worthwhile Fake Out Pokémon etc.