L4D, L4D2, Alien Swarm, Dota 2 and Portal 2 are in their own separate forks. You can see this if you poke around the file structure of Steam, and look for the dependencies for the various games.
The most used fork is still "Source 2009" which is basically just the Orange box era Source upgraded with Mac support. They constantly port features between forks as needed though, and sometimes remains from other games is in the wrong fork (I still spot TF2 console variables in Portal 2, unused). The most significant part about Source 2009 is how it still have dx8 support for legacy hardware, while that was dropped in the forked engines.
Interestingly, it might be worth to mention that Counter-strike Source used to be updated along Source 2009, but they stopped as a general engine update that usually came with the regular TF2 updates could sometimes be a nuisance for competitive CSS players.