Now, when I say "really clean tone," I don't mean that it has no distortion or gain. I mean that it sounds milky smooth, which usually results from lots of saturation. Some of Autopsy's work is kind of like that. It's hard to think of other examples, because when I think of cleaner sounds, I usually end up thinking of classic rock, which I'm not necessarily looking for.

Reminds me of the latter Death albums (Symbolic and Sound of Perseverance), especially for their audible bass tunes. However you must already know them. It's hard to make suggestion on just a production measure since I could tell you most metalcore do has "clean tones" while being "heavy music" with bands like August Burns Red. But sticking in the thrashy side the first few Overkill albums have really clean tones, that's what made them the masterpieces they are. Municipal Waste are very well produced too.

Looks like your question is too vague. If you can tell exactly what you are looking for... anyways, hope this helps.

Doom metal is probably the best example of that. Autopsy had a lot of doom in their older work.

Howls of Ebb may fit in your description: on their first full lenght they play a very dissonant kind of experimental death metal, but their guitars are incredibly clean and smooth for the standards of the genre.. also the album it's great and unique!

I'm jamming Howls of Ebb's "The Marrow Veil" and I'm really enjoying it. It's definitely along the lines of what I'm looking for. I think some other good examples would be early NWOBHM like Angel Witch's gloomier songs.

You should try the band Ouroboros from Australia.

i may be way off with this, but when you say you end up thinking of classic rock sounds, i'm thinking of horrendous' last two albums (especially ecdysis)

Is there anything softer in terms of distortion/tone? I really like the milky sweet tone of older electric guitar music, and a lot of these recommendations just sound too chunky. I think Autopsy's old stuff is the only thing that comes to mind right now, the guitars were really "softened" up by the production and saturation, to the point where it was almost cleaner than Sabbath's.

What about Cynic or Atheist?