2. Lex Luthor (Smallville)
Now, the comic book version of Lex Luthor - particularly the 'pre-crisis' era (prior to 1985) Luthor - might pose an intellectual threat to the Doctor (as I recall, he made a time machine out of orange juice cans, a piece of spring and a lightbulb in a jail cell), but the Smallville version of the character? Not so much. He's an intelligent guy, just not on the Doctor's level. One thing he does have in common with his comic book counterpart is his arrogance and self-obsession. According to Lex, the world revolves around Lex, period. The Doctor could identify this trait within seconds of his first encounter with Lex and, ultimately, exploit it as a weakness. As CEO (at different points in time) of both the LexCorp and LuthorCorp of the Smallville universe, Lex has been responsible for a lot of research in to super-powers and has created some very powerful technology. It's impressive stuff, but nothing the Doctor would be intimidated by, and nothing that the Sonic Screwdriver and TARDIS aren't totally ready for. Lex would be intrigued by the Doctor but, being Lex, he'd also think he was the Doctor's superior. The Doctor would prove otherwise.