I dont know about the secrets of Slashes Appetite for Destruction tone, apparently its not his usual amp though.. I'd like to know the secret :P
Tom, if you do a search on the Seymour Duncan forum there was along post on the subject kind of a year ago. Supposedly he used a mythic modded Marshall rented from I can't remember which company. Guitarwise I think it was his Les Paul replica.
Don't know much about tone secret either (apart from the above), but I am just listening to Blue Finger from Black Francis (the come back) and the sound he got from is telecaster is just brilliant. I think I am going to spend the afternoon with my tele to replicate it. After all his album The Cult of Ray is the reason I wanted a tele so bad for some years.
Other favourite tones of mine are Billy Gibbons on their last album to date (heard they were preparing a new one for this year) and on Tres Hombres (go figure what it was amongst the pletor of gear he is using), and Slash on It's five o'clock somewhere, which IMO is the best rock record ever.