Whoa, it's too hard to pick favourites as they are all great.
I love Mark's tone on the 2006 tour with Emmylou Harris. Even on songs like Why Worry, which he played with a capo in an ungodly position (8 fret or something), it still would sound like a dream. Les Paul was also great, Tele on one of Emmylou's songs was awesome. Can't even start to talk about the tone of the Romeo outro played on Pensa. Unbelievable.
This string of live shows — Real Live Roadrunning, Berlin 2007, and Prince's Trust 09.09.09 are masterclasses on tone, guitar playing and musicianship. Love it.
On albums, it's usually watered-down compared to live versions, so I would say my favourite tone on the album is Shangri-La.