Smallville
Time and Chance by Dayspring -- Clark/Lex. Mpreg. Beautifully written in exquisite detail and anguishing to read. Not your typical mpreg story as in Lex is the one who is pregnant. Dayspring is able to weave a tale you won't soon forget.
Three Important Things by Jenn -- Clark/Lex. Futurefic. Jenn is amazing, I cannot say enough good things about this story. It is a strong characterization of Clark going after what he wants and what he wants is: Lex! Let no one stand in his way.
A Handful of Dust by Jenn -- Kal-El/Lex. A/U. This has to be the most brutal story in the fandom I've ever read. Clark is not our Clark, he's for a lack of a better term, turned to the 'Dark Side. ' He has fulfilled Jor-El's wishes and rules the world. Lex is the leader of the resistance and Clark's former lover. Clark will stop at nothing to get Lex back. This is the story to read if you are new to the fandom!
Family, Friendship and Love by Henry Jones, Jr. -- Clark/Lex. Mpreg, kidfic. Don't let the labels scare you off, this story is lovely and heartwarming. Henry Jones takes Clark and Lex's child and gives him a personality that doesn't make you want to kill him! It is also about Lex and Clark learning to love each other again. I read this story at least every three months.
That Old Schizophrenic Jealousy by Lenore -- Clark/Lex. What would Clark do if Superman started having sex with Lex Luthor? He's become a little bit unhinged and jealous, that's what. Lenore writes brilliantly and this story is a gem!