Regarding good "Smallville" fanfic - one of the best I've read was written quite early on in the run of the show, after only 2 or 3 seasons on the air. The major villain of the story is Lionel Luthor, and Lex is still a guy who could go either way (and, spoiler, chooses to be on the side of good in this fic.)
The fic is
Elsewhere by bulbus, and I strongly recommend it. It's got plot, action, drama, and people making choices. Plus a whole lot of Supermanly heroics.
