[Warning! Inexpert opinion follows! Experts feel free to correct any misconceptions intruduced in the following text, but be nice or I’ll accuse you of trolling! ;)]
To tell the truth, I think it’s pretty simple. A troll is someone who deliberately tries to start trouble (usually an argument) on a BBS or in a newsgroup. A troll is deninitely not someone who simply disagrees with you. They go beyond that by being altogether disagreeable. The intent is to start a flame war (or some similar unpleasantness).
I think the name was arrived at because the verb “to troll” means “To fish by trailing a line, as from a moving boat.” Additionally, a troll is a rather disagreeable creature found in fairy tales and fantasy role-playing games.
–Baloo