I ALWAYS knew it!

[frag.machine]

But... where does fit Quake guy ?

[Dr. Shadowborg]

O_o

I would have thought that this was already well known by now...

As far as the Quakeguy is concerned... I would say that he isn't related to them given the demonic apocalypse of Doom 2. (And the apparent lack of comment in Quake about such an affair, Portal / Slipgate research would likely have been banned for obvious reasons...)

Parallel universes are likely involved here though, and I suspect that a convincing argument could be made for Quake and Quake 2 being somehow connected, given the "Winged Skull" logo on crates. Maybe the Strogg are the result of Gremlin experiments on Grunts and Enforcers? (It's too bad the "built-in blasters" thing that the manual mentions doesn't really appear to be the case on the Enforcer's model.)