Ponder on what your story is about, then go for something meaningful.
Simple example: Ellie Arroway, in Contact - a reference to David Bowman from 2001: A Space Odyssey, as well as a homage to Eleanor Roosevelt and Voltaire (real name François-Marie Arouet)
Complex example: Thomas Anderson (aka Neo) in The Matrix. Anderson means literally "son of man". This refers to Neo's messiah-like condition ("son of man [http://en.wikipedia.org/wiki/Son_of_man]" being Jesus). However, Thomas means "twin", which implies that he is not unique as a savior (which is eventually confirmed). It also refers to "doubting Thomas", meaning it will take until the very end for Neo to believe himself to be the One. You really can have a field day hunting down mythical/metaphysical/philosophical references in The Matrix.