MISSION IMPROBABLE : The wonderful mod made by Magnar Janssen telling the story of Gordon investigating a Combine lighthouse and then helping rebels has unfortunately no place in the official timeline... However...
SPACETIME CONTINUUM OF MI : If we consider the alternate timeline of Coastline to Atmosphere and Strider Mountain, it can fit well after both of them. It can be trusted since no major characters appear in MI.
RESEARCH AND DEVELOPMENT : The "best HL2 mod of all time" telling us the story of some guy with no weapons in a combine and zombie infested experimental base called "NERDZ" can fit in the timeline with some explanations.
SPACETIME CONTINUUM OF R AND D : Sometimes during the gap between HL1 and HL2. I guess some weird looneys (the so called "nerdz") created a base to make strange games for their own personal amusements, capturing Combine so they can fight some poor "players".
DANGEROUS WORLD : The infamous mod about a rebel starting just after the Dark reactor's destruction to the Citadel fits well in the official timeline, going so far as being paralleled with moments of Episode 1.
SPACETIME CONTINUUM OF DW : Can be considered canon and in the same time as Episode 1.
EYE OF THE STORM : The sadly unfinished mod of Lord, in the City 14 with its own administrator, and some Ravenholm at the moment of its fall.
SPACETIME CONTINUUM OF EOTS : Before HL2 because started with the "Ravenholm" mod not yet Zombified then going into another City ruled by Combine. Sadly, it ended in part 2 in an unfinished note.
HUMAN ERROR : A "play as combine" mod where you start with an intro during the Portal Storm then you're put as a Metrocop exploding Vorts and Rebels.
SPACETIME CONTINUUM OF HE : As some Xenians are still presents on Earth and the Rebels are crushed, surely before HL2. So : Intro just before the 7 hour war and then before HL2.
COMBINE DESTINY : Another "play as combine" mod where you blow the hell out of Rebels and zombies.
SPACETIME CONTINUUM OF CD : After the 7 hour war and before HL2.
COMBINE COMBAT : Another "play as combine" mod, sadly unfinished, where you play a Metrocop tasked to kill Gordon Freeman. Cool mod, besides.
SPACETIME CONTINUUM OF CC : During HL2 and after "A red letter gone wrong".
CALAMITY : A mod where you are ordered to guide a Rebel train to a Combine structure to blow it up. Good mod ending with a TWIST ---->
SPACETIME CONTINUUM OF CALAMITY : As revealed in the climax, an "alternate timeline" set in HL1 when the Spectrometer exploded triggering the resonance cascade and sending temporary Gordon in the future to blow up a not-yet constructed Citadel, before returning back in time in HL1 in "unforeseen consequences".
FORWARD MOTION : A strange mod/mappack starting with some Combine to blow up in City 17 then switching to a mystical land where you have to activate some ancient artifacts, and with that, you have to flee a floating corpse pursuing you with a wall of death...
SPACETIME CONTINUUM OF FM : Dunno. Looks like a rebel during HL2 getting teleported on an alternate dimension.
RANDOM QUEST : A strange and interesting mod where a man walking on the streets is teleported to a medieval castle ruled by a Vortigaunt and some humans, then an arena with Antlions Guards, some looneys on a lost land, and ending with a cliffhanger after blowing some other crazy humans.
SPACETIME CONTINUUM OF RQ : It can fit!!! After the Portal Storms, some guys is caught in a dimensional vortex and ends in a world where some "renegade" Vortigaunts, freed from the Nihilanth, rule this world and some exiled humans either serving the Vort's, or having become crazy.
That's it for today : Next episode : THE CITIZEN, GET A LIFE, ... And others.