Ok, I'm going to summarize what I know:
L4D is the main universe (alternate path of reality, so to speak)
TFC and TF2 are in the same universe; confirmed by TF2 engineer's dad being TFC's engineer
The CS series and DoD might be in the same universe but that's up to Valve to decide, I figured they're war games of real-life battles (WW2 and USA's War on Terror) so they would be in that vein; however:
CS, Ricochet and Deathmatch Classic are (at least by the Steam store pages) to be in the same universe, at different points in time.
The HL series and Portal series are 100% confirmed, Portal references Black Mesa several times and vice versa.
And finally, Alien Swarm is more likely than not in it's own universe.