In Fallout 2 I didn't know that a bug prevented the happy ending for Gecko from happening if I optimized the reactor after fixing it, even doing everything to make it happen. If I knew it, I would have just fixed the leaking reactor. Those poor ghouls were eventually made slaves by Vault City.
Also I fucked both Bishop's wife and daughter, getting just the latter pregnant, IIRC, but I messed up something, I don't remember what, and the mother of my son always held a grudge against me from then on.