Phoenix Warlords, Celestial Dawn and Battlers Pride are big ones, probably the "top 3" (though the order changes depending on which one wins which event). And of course people will argue about this -- I saw a neoboard thread once asking which BD guilds were the top ones, and it started an argument.
I'm in Battler's Pride, and when I was an active player, it was a very good guild. They do a lot of in-guild battling, too.
BP has a rule of thumb that you had to have at least one pet who's battling stats (HP+STR+DEF) added together is greater than or equal to 200, so most of the players in there are fairly serious about the battledome.
Anybody have any information on who to contact in order to get into one of these guilds? My current guild is pretty much dead, and I think it is about time to start exploring my options...
Many BD guilds have recruiting threads on the battledome neoboard, so watch for one of those -- you can ask questions about the guild or request an invite. They will also specify if there are any requirements you need to meet. For Phoenix Warlords, the rule is that your strength + hit points has to equal 200 or higher.
I am in forgotten warlords. Its a little smaller but has a few big names. Its reativly small size makes it easy for people to socialize and get to know each other which is really amazing.