Shoddy has been out for a couple of years, like UT. Still fun though! Some servers already have the Black/White pokemon, and custom "create-a-pokemon."
Download it here:

http://shoddybattle.com/

Pokemon Lab is the sequel to Shoddy battle, just released. I like this one.

http://trac.poke-lab.com/


There's another new one, but I don't like it as much:

http://www.pokemon-online.eu/


Any teams you make on Shoddy can be imported to PL or PO, so I'd suggest trying Shoddy first.

Shoddy and pokemon lab are both out dated now. Pokemon Showdown is the new hotness.

http://pokemonshowdown.com/