i'll give two examples, one being my way with their amps the other being their way.
my way:
Laney Gh50l-
Presence 4.5
Resonance off
Bass 7.5
Mids 6-7
Treb 6
Gain 6
Drive 7
Boss GE-7 in the fx loop with the settings in a shallow V with the center mid freq bumped just above neutral. Throw in a light delay and it gives a nice addition to the sound.
personally...I think this sounds better then their distortion live, but you lose a lot of versatility plus good clean soo..
their way-
Laney GH100l (same thing, more watts)
Presence...not sure on this looks like about 4-5
Bass 0
Mids 9-10
Treb 0
gain 4
drive off
GT-6 in the fx loop with god knows what settings, but I think something like the 5150 amp model with eq settings similar to what I used above and probably reverb/delay. I was never quite able to nail it with a GT-3, hence using the other method. But the clean settings are easier to get and work very well like this.
biggest thing is a good guitar with good pickups, the SD JBs that they use work great, let a lot more ring out on those chords. If you have cheap pu's it will be muddy, and if you have too much gain (EMGS) you get the same thing (but heavier at least). After that it's keeping the gain down, and if you're using just an amp the EQ in the fx loop is the secret weapon...for any type of sound. The rest is playing style, which really does make a difference but i'm sure anyone who has worked on opeth songs enough starts to notice the little nuances thrown in to the guitar work that makes it sound that much better.