Which escort mission, exactly?

Heh, pretty much the first one :D The one right after you meet the concealed human colony, the fleet separates into two parts - one tries to reach a jump node and the other distracts Shivans at another jump node, and (well... Obviously) not even a single ship can get destroyed. The biggest problem I have with the mission is that it throws bombers at you from all sides and I can't even get to the other side of a ship I'm protecting in time, let alone shoot down the bombers.

Ah, yes. That one. Yes, it is pretty tough, because you need to make good use of all the wings under your command . Have your bombers destroy any Shivan cruisers threatening the convoy and keep all other wings assigned to your cap ships. And, yes, pack enough trebs. If the Lilith class cruiser shows up, destroy its main beam cannon with two trebs ASAP. The mission basically expects you to be in the right place at the right time. It can be done, though. Just save enough trebs for the last part of the mission.

How do mods in Crysis work exactly? I'm getting a new computer this summer, and I was planning on playing Crysis with the Extreme Quality Mod. Do they affect the single player campaign, or are they only for additional maps and levels?

Oh god this one's AMAZING, fantastic feel of unseen danger - even thou I know for a fact that there are no monsters, I even jumped several times because of weird shadow or falling debris. And I was in a completely lit room with my wife watching TV right next to me! Saved the game at the beginning and now I'll play it when wife's not home. Great stuff, thanks for suggestion
I've tried installing extreme quality mod (now it's extreme immersive mod) - it actually comes with an installer and stand-alone launcher, so no trouble there. As for The Worry of Newport, you can install most bigger mods on MODDB using their distribution service Desura - you just press 'Install' and Desura does all installation and configuration for you.

The ones that immediately come to mind:

Counter-Strike
Day of Defeat
Action Half-Life
Rocket Arena - Quake 3
Urban Terror - Quake 3
T2X: Shadows of the Metal Age
The Nameless Mod - Deus Ex
The Dark Mod

Aliens Total Conversion for Doom.

That was creepy x_X

Just tried Red Alert mod for Red Alert 3. Fantastic recreation of RA skirmish, with AI using all strategies and using superweapons and all. It also got original voice acting and music and ... Well it's awesome.

Garry's Mod.

T2X, CoSaS for Thief 2
Derelict for Freespace 2
Brutal Doom for Doom
Paranoia for Half-Life
Out of Hell, Hollow Moon for UT 2004

Why not? No time?

My best mod was probably Empire and Federation for Star Trek Armada. It was a total conversion that changed the game from a Next Gen era game into a TOS era game, including adding the Gorn (remember those lizard guys from the episode where Kirk builds a canon out of stuff he finds lying around) as a playable race. At the time, it was the most polished and professional-looking mod I had ever seen, plus it was a ton of fun to play.

Oh no question - I'd classify several scenes/events almost as homages to the new BSG series they're so close. Because they are so close, in many ways it does seem more like an homage of respect than stealing them somehow. Or maybe because the final product was so good, stealing those scenes and ideas from BSG does honor to them so I'm happy they did it. There are also several other clear influences in it - a little Babylon 5 in the ship design and philosophical themes (especially in the previous game Age of Aquarius) for instance. It's been awhile but I remember more.

But as you say, the important bit is that the mod is awesome. :)

My favorite "mod" too.