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 engineerThe 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.
I'd like to add that, since Louis references to CS and HL2, they're still just games in their universe (our alternate reality, as you said).
Ellis also references TF2.
I'd say the Half-life series and Portal series are related, but Portal is less dark and I'd only consider the Borealis cannonical. Day of Defeat and Counter Strike could have a similiar universe. Team Fortress Classic and TF2 could be similiar if you count the picture of the TFC Engineer patting the TF2 engineer on the head.
Can you show me that picture?
