When XFree86 restricted their license in 2004, the result was a fork into the dominant X window manager we know today -- X.org. At the time, just about everyone was pissed off at XFree's sheer arrogance. Thankfully xorg and freedesktop.org pulled everything together and in very short order (relatively speaking) all the major distributions swapped their X server. I mistakenly thought at the time that the progress in the X server would digress -- that forks were disruptive to software development.
While I was wrong about that, I think the split between the two leading 3D linux desktops, Compiz and Beryl, was very counter productive. I was glad to see that many of the passionate differences had been put aside when they announced that the two forks would be merging back together. There was a lot of great work going on in both camps, however I've never seen such discontent and bickering between two factions. Given the obstacles that 3D desktop faces (poor driver support, chipset differences, etc.), everyone would benefit from cooperation rather than reinvention. Even with this division, I'm really impressed by the quick progress they have made to get things working.
While I still have yet to get either to work with my laptop's ATI chipset (damn you AMD!), I really can't wait to get it working on my next computer. It really is one of the more exciting things that will set Linux apart from Windows and Macs.