The obvious one is astolat's Reconcilable Differences. After a serious injury that leaves Kon paralyzed from the waist down Lex forces him to live with him to get physical therapy and the use of his legs back. It's Clark/Lex with a hint of Tim/Kon. Mostly, it focuses on Kon's changing relationship with Kon, until about midway when it focuses more on Clark/Lex.

This one is AU and Tim/Kon. Scions by winterlive. Kon is Lex Luthor's son, Tim Bruce's adopted kid. They work for their father's companies and meet when both Luthercorp and Wayne Biotech want to buy the same company (Cadmus).

Both are more Smallville than comics and Scion is mostly about Tim/Kon, but there is a scene where Clark gets involved and he and Lex have to clear the air between them somewhat for Kon's sake.