Nerd - Very similar to the geek, except with a greater focus on high intelligence. Usually more concerned with science and computers.
Geek - Someone who is generally socially awkward and identifies with a particular subculture, usually involving science fiction, anime, video games, fantasy, and other non-mainstream genres. Generally associated with above-average intelligence.
Freak - Strongly negative connotation, unsettlingly strange, possibly dangerous or mentally ill. Can also mean the person is extremely sexual, good in bed, and possibly engages in abnormal sexual practices. When used in this way, it tends to have a positive connotation.