I often discover several locations on my way somewhere, and only later do I get around to properly dungeon delving into them....only by then I don't remember which I have actually looted/explored, and which I just breezed past. And I certainly can't remember when I'm on to a second character. So in the end I often never really get around to going INTO many of the dungeons because I think I already have.
I would be thrilled if there was just a way to change the map marker icon to a "third" color signifying "done" or fully explored (or whatever anyone wanted it to mean, but that's what I would use it for).