I highly recommend the Renegade Commentaries, the grand-daddies of the alternate commentary: http://www.renegadecommentaries.co.uk/

I really like Robert Altmans commentary on M.A.S.H. That guy was a movierebell before it was cool.
The commentary on Steve Zissou by Wes Anderson and Noah Baumbach is VERY entertaining.
Jean-Jacques Annauds commentary on The name of the rose is one of the most informative traks I have heard.

The best one I ever heard, not the funniest, not the actors mucking about, trying to crack each other up ( I hate that shit), ws the first I ever heard, Martin Scorsese's track for "Taxi Driver" back on the criterion lazer disc. To me that's what commentary tracks are all about.
Also have you heard Jack Hills and Quentin Tarantino's commentary track for "Switchblade Sisters"? One, it's not a yuck fest which is good. But it's really interesting, because Quentin really likes the movie and keeps making a case for both the film and Hill's technique. But Jack Hill seems a little embarrassed that Switchblade Sisters is all he has to show for his career.
Also I've always been a fan of Jeff Leiberman, and his commentaries on "Squirm" and "Once before Dawn" are terrific.