Do cues that were recorded specifically for the album by the composer count?
If so, "Adelita" from THE WILD BUNCH.
More in line with what I think you're looking for was when I discovered that cool pirate raid action music in THE ISLAND was not Morricone (and I knew it sure didn't sound like him), but was Richard Strauss' "Ein Heldenleben".
Maybe not a favorite one but I did like the "Main Title music" from Sixteen Candles and for a long time I thought it was by Ira Newborn.
Speaking of "Main Titles" then what about Walter Werzowa`s Main Title film version from Eraser? How come that this version was not featured on either the original soundtrack album or the expanded released?
I suspect that the late Johann Johannson would have been dismayed to be congratulated for tracks that weren't his -- "Arrival of the Birds" in THE THEORY OF EVERYTHING and "On the Nature of Daylight" in ARRIVAL.
When watching the trailer of "The World of Henry Orient" there is a short musical cue heard that always catches my attention. Its not in the film proper nor was it included in FSM's CD release. I still haven't been able to track it down where it came from.