Clean glass MAY be one indication of clean burning . . . much like black glass MAY be one indication of burning that is not clean. Other indications of a clean burn would include a good sustained secondary burn with a secondary burning stove, no smoke coming out of the chimney and of course the end-all, be-all indication -- what the chimney looks like in terms of creosote.
Small fires early in the year can mess up the stove . . . often temps are not getting hot enough . . . draft isn't overly strong . . . and if there is any black or brown the fires may not be getting hot enough to burn the stuff off. Burning later in the year often clears up this problem.
Pine and softwoods . . . I don't get blackening from this wood . . . but I do often get some pitch spit on to the glass as the wood heats up and the pockets of pitch (especially on the fir) hits the class and leaves little smears . . . this is cooked off however once I get the stove up to temp and the magic begins . . . by magic I mean secondary burn . . . magical unicorns do not start frolicking around my living room once the stove is up to temp.