SiN, DDH, Combine, The Regulators, The Mercs, Something Awful aka Hordes of Goonheim(newbs but a TON of them). Ummm LotD has a lot of members it seems.
A lot of WoW guilds that are supposed to be "new school PvPers" I don't recognize any of them because I haven't ever played WoW... but they don't seem to be any good.
I know I am forgetting some that I have seen a lot of.... ohh KAAOS is here. Umm shit I know there are others. There is an "official" list here http://www.aocsource.com/showthread.php?t=717