This program is AWESOME, somewhat of a pain to install, but a pleasure to use (and it's free).
It has a very advanced algorithm underneath. You "train" it so it learns what you consider spam, and what you consider "ham" (good messages). For laughs, here is a (real) excerpt from the description on how it works:
An example: a message with internal spam score that's 50 standard deviations on the spam side of the ham mean score and an internal ham score that's 40 standard deviations on the ham side of the spam mean would, if you just combine them in a straightforward manner, produce a result that it's definitely a spam. But look at the internal scores - it was certain that it wasn't spam, and it wasn't ham, either. In other words, it's not like anything it's seen before - so the only thing to do is to punt it out with an 'unsure' answer.