1.08 because of the awesome super form back then and the nice untouched features. 1.09.2 was a bit more limited than 1.08, but in 1.09.4 got a hell load more features, and was 1.09.4 definitly the most active version EVER. I liked all the little tricks, glitches, and replayability we got from them. Especially not to mention thanks to all the many wads, mods, and ports we had back then. Awesome. I prefered the entire Match and CTF systems and stages loads more too.
I'm gonna have to say 1.09.4's still my favorite, second favorite being 2.0 tied with 1.08. SRB2 2.0 just didn't grow as far as 1.09.4 yet, and misses many nostalgic features and wads of that version.