Standard Clauses
Uber Clause: The following pokemon are deemed to be unbalancingly powerful and are not allowed to be used: Arceus, Blaziken, Darkrai, Deoxys, Deoxys-A, Dialga, Giratina, Giratina-O, Groudon, Ho-Oh, Kyogre, Kyurem-W, Lugia, Mewtwo, Palkia, Rayquaza, Reshiram, Shaymin-S, Xerneas, Yvletal and Zekrom.
Update 12/21/13
This is going to be our initial Uber list, and as such is subject to change as further battle testing is done. Be sure to keep an eye on this thread as so more Pokemon may be added to this list as time goes on and others may be removed. Banned Items: Gengarite and Kangaskhanite
Self KO Clause: Your Pokémon cannot use moves like Explosion or Self-Destruct to win if it's the only Pokémon remaining on your team. The same applies for Perish Song and Destiny Bond.
Sleep Clause: The sleep clause means that you cannot put 2 enemy Pokemon to sleep at the same time. This means, if you put my Gengar to sleep, and I switched out for Arcanine, you cannot put Arcanine to sleep until Gengar has woken up. However, if you KO the sleeping Pokemon (Gengar in this case), feel free to use your sleep moves again. Please note, that Pokemon who have induced their own sleep, commonly through using Rest, then that does not count towards the clause.
Evasion Clause: One of the most questioned clauses, but it's right up there with Uber and Sleep for importance. Basically, this clause means you cannot use evasion increasing moves like Double Team and Minimize. This clause has appeared due to the fact that any Pokemon who can use TMs can learn double team, and there's no way to get rid of the evasion bonuses except through the move Haze, or if the opponent switches out. Further leading to the unfairness of double team is the fact that after 2 uses, only about 60% of your attacks can hit the foe at all and to finish it off, double team can be baton passed to a stronger, faster or sturdier Pokemon.
Species Clause: This clause means you can't have more than 1 of the same Pokemon (or any of it's same evolutionary chain) on your team. This is mainly used just because it's kind of annoying to see 4 Garchomps or a Charmander and Charizard or something ridiculous like that. This clause is oftentimes not used, but will normally be active during tournament play. This clause of course does not effect the use of multiple Eeveelutions or any other pokes with optional evolutions.
OHKO Clause: Moves like Fissure, Guillotine, Horn Drill and Sheer Cold are banned from use as the only surefire counter to OHKO moves is to have a focus sash/focus band, an ability that prevents them, or to not get hit by them. While some may argue there's only a small chance of getting hit by them, this only makes it even more frustrating when a player that's better than another loses. Because moves like these require more luck than skill to use, they are typically banned.
Moody Clause: The ability
Moody is banned from use.
Endless Battle Clause: Any moveset on any Pokémon that is capable of intentionally causing an endless battle is banned from competitive play. Specifically, it is banned for a Pokémon to hold a Leppa Berry and carry Heal Pulse, Recycle, and a recovery move (Milk Drink, Moonlight, Morning Sun, Recover, Roost, Slack Off, Softboiled, or Wish) on its moveset.
Update 12/21/13
The goal of the clause is to ensure that strategies able to create an endless game—one that only ends when the opponent's Pokémon have all been PP stalled or he or she forfeits. Currently, this clause only encompasses the use of Leppa Berry, Recycle, Heal Pulse, Block/Mean Look/Spider Web, and a healing move (such as Recover or Softboiled) in the same moveset. This is how it works:
Fortunately only Slowpoke, Slowbro, Slowking, Blissey and Smeargle are legally able to use this combination (Ralts, Kirlia, Gardevoir and Gallade as well if you count Wish). To use the strategy, one of these will switch into a defensive Pokemon, or one unable to 2hko them, use Block and then PP stall the opponent with recovery and Leppa Berry + Recycle. Once the opponent begins to Struggle, the user can simply continue to Heal Pulse, with Leppa Berry + Recycle, until the opponent forfeits.