Pretty much all of Lieutenant Ash's lines in the FS1 intro. The fear and panic in his voice was perfect.
I definitely have to agree with that. The way he was shouting literally gave me chills the first time I saw it...
As for individual lines, well, for some reason I always really liked that cutscene where the scientists test the shield system. If nothing else, the Back to the Future reference ("Power levels holding steady at 1.21 gigawatts") was brilliant.
And for pure comedic effect, with all due respect to Mackie--whom I thought was awesome--I have to hand it to Microsoft Sam for his awesome attempt to pronounce "Llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogoch" in the first mission of Deus Ex Machina.