One who
thinks for themself in the manner they wish to, despite external pressures. As much about one's
methodology or
thought process as it is about their individual
opinions. One who thinks outside the
intellectual status quo.
Thought crime.
Today you needn't be a free-thinker to be an atheist or a humanist. Hell, in some parts of the country it's easier to be a libertine than an honest, god-fearing American.
Hell, as long as you're ready to be a sheep for the cause, you can hold any viewpoint you want without having to be yourself. Not only that, but you can pretend to be a free-thinker.
Just don't cross the science guys. They'll (ironically) (and meta-hypocritically) tell you to think for yourself (and agree with them).