I really like the tone on Opeth's Lamentations DVD. Especially on "Master's Apprentices". Porcupine Tree also has really awesome tone on both studio albums and on the live dvd.
I also like Devin Townsend's tone on most his stuff.
The lead tone on tools parabola, during the second lead run. Its like back and forth between super saturated singing tone, which blooms into sawtooth waves, and back again
Say what you want about the band, but Slipknot's tone on Iowa is pretty cool. It's not how I would have dialed in the VHT (I believe Mick used a Pittbull on that), but it sounds great.
I also really love Machine Head's tone on their last 2 albums, as well as on "The More Things Change...". Also a big fan of Behemoth's Mesa tone on "Demigod" as well.
In terms of classic rock guitar tone, it does not get any better than Queen or Blue Oyster Cult IMO.
Here's one that no one has mentioned here: Martin Barre on Jethro Tull's Bursting Out album - that tone just screams classic British rock. Very underrated guitarist, too.
Hmm, actually I think my favourite distorted tone would have to be something like brown sound except slightly more high gain. Probably like the intro of About to Crash by DT.