My favorite story is
Breaths of Passion, for two reasons. First, I never felt there was a good basis for Lex's obsession with Lois and a lot of the series hung on that obsession. I could see Lex wooing Lois as a way to one-up Superman but a psychopath wouldn't have any problems cutting his losses when his self-interest is at stake. It would take an obsession to drive Lex to the edge and beyond and I think the story gives a plausible explanation that doesn't contradict canon. The second reason I like this one most is that I think I kept Lex true to character in the story, which has always been hard for me.
