"Cogs in Motion" definitely counts. It's like something out of a factory scene in a silent black-and-white 1930's cartoon, which makes it awesome.
Jurgen's Lair Suite qualifies, too. Come to think of it, the series has a dozen tracks like this, particularly in season two and DEFINITELY in season three.
I couldn't find anything to link to "Fugue and Dies Irae," but that has to be my favourite song of all.
According to composer Jared Emerson-Johnson, each of the Telltale episode contains as much music as an average 30-hour console title. So these games are really concentrated with music of awesome.
And this is the reason of why Telltale release Soundtracks of this games
The theme for The Devil's Playhouse certainly counts (starts at about one minute in).