I find that I get a pretty close Opeth sound with my rig.. Clean and Distorted
-2002 Gibson Les Paul PP (BB Pro's.. I know these are vintage pickups, but I can dial in amps correctly)
-5150 Combo (on rhythm channel, use crunch switch for leads)
Fender Hot Rod Deluxe (cleans, any fender amp will do the Opeth clean sound on the bridge pickup of a mahogany guitar)
Mike uses the Full Shred/Full Shred combo in his guitars. You can tell because they are the allen head pole pieces. It seems as if Peter might have the same set in one or two of his guitars, but most of the time it's the Dragon II (stock in most PRS). I find that having a decent pickup in a mahogany bodied guitar through my 5150 will create Opeth if you have the chops!
This setup gets me closest to Still Life's distorted tone. (They used Les Pauls and 5150s for rhythm work on that album.. also on MAYH
). Again, the clean tone is really nice, but if you got the chops you can make it work on any decent vintage-like clean amp.
I also have a Mexican Fender Strat that I hot-rodded by changing pickguard, pickups, knobs, etc.. but I put a high output bridge humbucker in it (Custom 5). It definitely gets more of an Opeth sound with a higher output pickup, but in the Alder it's a little shrill for Opeth. You could probably associate it with more of the nasally midrange of Orchid and Morningrise. I love the tone on these albums though! Don't get me wrong! Just more of an "effects" pedal distortion.