I always thought it was a bastardization of 'root' a'la hacker speek. There's a few more links here:
http://pool.dylantree.com/pool_faq.php (see item #7)
Lifted from the Dylan forums aforementioned:
"Some of you may be interested to know that "woot" is a middle english word, meaning "know".
A SHIPMAN was ther, wonynge fer by weste;
For aught I woot, he was of Dertemouthe.
(Transl: There was a shipman, dwelling far in the west;
For all I WOOT, he was from Dartmouth.)
(Chaucer, General Prologue to the Canterbury Tales)"
AND:
"it's an ancient Dutch greeting........... from the word "woeten", which meant "to greet"......... similar to "groeten" in some of the more "maintstream" dialects........ over time, the "oe" got slurred, and it became "woot"............. as in "woot! hoe gaat het?""
-Zeke