On the crazy glitchy Head of State quest, I was just about to bring Caleb back a photo of the Lincoln Memorial. Unfortunately, the game decided at that moment to spawn some radscorpians on me and the free slaves. So, Caleb and a few others go out to kill the radscorpians, and I panicked, knowing that they would get killed and I would be screwed over for finishing the quest.
Well, I followed them out, but I didn't get there in time. Caleb got killed, and now I have an unfinishable quest in my log. It's quite annoying, actually.
Another one was with my law bringer perk. I went to their outpost, and while I was inside, they started reacting to a radscorpian attack. I had read about this before, saying that Sonya could just book it into the wasteland and I'd never see her again, so I did my best to kill off the radscorpians. Too late- again. Sonya took off, leaving me with a hell of a lotta fingers that I couldn't cash in for caps. I wasn't too pleased, to say the least.
Oh, and one more. I was in Evergreen Mills, and I acidentally fell down into a crop of rocks. I was stuck there, and couldn't get back out. Plus, there were two raiders within my perception distance, so I couldn't fast travel. I tried to kill them, but they far above me on a bridge, and were walking roundabout routes. It was extremly frustrating, because I ended up having to load my last save.
Fun times with Fallout 3.
Despite the glitches, it's still one of my favorite games.