This was a recurrent problem in mods, especially good mods we like, we love... we consider it "Valve-like" qualities, and we would like for them to be considered "canon", even if official add-ons such as Blue Shift and Opposing Force aren't considered really canon by Valve themselves.
Through the upcoming parts of this blog, I will try to make explanations on some well-known mods, both HL1 and HL2, on how they fit with the HLverse.
1) THEY HUNGER : We know during the storyline that the zombies where created when Dr. Franklin discovered a strange substance on the waters surrounding the small town.
My guess is that during the Portal Storms following HL1 and a little before the Seven Hour War (admitting that it happens some months/years after the BM incident), some alien organism infected these waters, a specific organism allowing the dead to come back to life.
SPACETIME CONTINUUM OF THEY HUNGER : Shortly after HL1 events, on an isolated American town. Maybe a town not touched by the 7 hour war, cut from the rest of the world, in a sense.
2) AFRAID OF MONSTERS : Nothing special. Some addict in a town without nothing specific on the HLverse.
SPACETIME CONTINUUM OF AOM : Before the Black Mesa Incident since the world wasn't screwed at this time.
3) USS DARKSTAR : Tough one. We can guess that some sort of human-like "aliens" discovered planets full of Xenian Life and then all hell breaks loose.
SPACETIME CONTINUUM OF USS DARKSTAR : "In a galaxy far far away", before or after the Black Mesa event... Not really important for the time.
4) TIMELINE 1, 2, 3 : An interesting one. Gordon is recruited by the Gman to travel in time and save the world from nazis, but at the end Gman betrays him to work with Hitler and as a result Gordon destroys the crystal of time, and every event is erased to go back in time just at the HL1 beginning.
SPACETIME CONTINUUM OF TIMELINE : Alternate timelines from HL1 ending to during some years, then everything is erased as nothing happened.
5) ABSOLUTE REDEMPTION : Gordon being reactived between HL1 and HL2 to do some things on Xen and on an Earth not yet "enslaved". No special "temporal paradox".
SPACETIME CONTINUUM OF ABSOLUTE REDEMPTION : Gordon out of stasis before the 7 hour war, on Earth and Xen for a short time before being re-put back on stasis by G-Man.
6) BLACK OPS : Nothing special, Declan Walker fits well in the timeline.
SPACETIME CONTINUUM OF BLACK OPS : Shortly before HL1, then during HL1 and OpFor, and ending shortly before Black Mesa being nuked.
7) ZOMBIE EDITION : Again, nothing special, just a nameless zombie doing some stuff during the Black Mesa event.
SPACETIME CONTINUUM OF ZE : During HL1 events, after Resonance Cascade and ending when the nuke explodes.
8) POINT OF VIEW AND AZURE SHEEP : 2 great mods taking place during HL1 events with no problems with the timeline.
SPACETIME CONTINUUM OF POV AND AS : After Resonance Cascade and ending before the nuke.
9) CLEANERS ADVENTURE : a mod with an HL1 janitor. I can't really understand the ending (since it's russian) but I assume the hero is either dead or taken in Gman's custody.
SPACETIME CONTINUUM OF CA : During HL1 events, before Resonance Cascade and ending before the nuke.
10) CASE CLOSED : a mod with a poor lawyer visiting Black Mesa at the wrong time. Again (and again..), some random guy lost in the giant complex and fighting his lot of aliens and grunts.
SPACETIME CONTINUUM OF CC : During HL1 events, same as Cleaner's adventure.
And so that's it for the first part!!! check out the sequel(s)!!!