Currently, what is on GW's websie is what is official.
Soon to be published is FAQ2010 (a little behind schedule), and a whole host of modifications to the existing fleet lists. These can eb found in a link in flybywire's forum signature, but won't be official until they are posted on GW's website.
Of fan made modifications, the two major ones right now are:
Eldar MMS v1.9, which fixes the way eldar play. Right now in the hands of a skilled player Eldar are effectively unbeatable. This fixes that, and makes them more fun to play as and against.
Fixed Ships (or FS), which is being developed in parrallel to FAQ2010. FAQ2010 barely touched on rebalancing ships that needed it, so this is a fan-made rebalance. It extensively rebalances the ships of every fleet, includes Eldar MMS v1.9, A complete overhaul of Orks, and adjustments to the core rules to correct things that couldn't be ammended in FAQ2010. it's in development at the moment, and links are in Plaxor's signature.