In the summer of 2003 the most self-aggrandising such troll organization was the "Gay Nigger Association of America", part of the Slashdot trolling phenomena. It was engaged primarily in moderating its own posts upward.
Usenet readers will likely recall alt.syntax.tactical, a troll newsgroup whose stated purpose was to discuss trolling techniques and organize raids of other newsgroups, basically to attack the signal-to-noise ratio of the other newsgroups.
A somewhat quieter organization, the (Meta-Wikipedia) Legion of Trolls, attracted a few anarchy-minded Wikipedia contributors. Most had contributed many serious articles, but apparently saw declaring themselves to be trolls as a political statement. There is some correlation between those who made this declaration and those who helped document the Wikipedia power structure. This suggests a longer term plan than for instance the GNAA would likely be capable of.
Other troll organizations are rumoured, but none have so far been announced.