When I lived in Billings back in 1987, I fished the Stillwater a lot, all the way up into the forest. It is a little gem of a river that when I was there was little known outside of the local area. I suspect in large part because it is a smallish river that was not floated by the guides when I was there. I don't know if that is still the case since I moved to WA State in 1991.
I also used to fish the Bighorn just about where the Bighorn Lodge now sits below the bridge that goes to Crow Agency. The Bighorn in that area was a terrific fishery and very few folks bothered to fish it then. I would imagine that is no longer the case since the lodge was built in about 1990.
The upper Boulder was another place I liked to go. And I used to fish the Yellowstone from Laurel all the way into the park below the falls. The Gardener is another of those little gems, even though it right next to the entrance road.
I have many found memories of the Lamar and the Clark Fork just outside the park as well. The Shield's was another little gem that never seemed to have many fisherman, as was the upper Judith.
When I left Billings, I moved to Boulder and was within an hour of the Missouri at Craig, Big Hole, Ruby, Upper Clark's Fork, Jefferson, Madison both above and below the dam, Little Blackfoot, Blackfoot (and I remember very well the massive fish kill on it when the 100 year old 7-up Pete tailings ponds failed). The North Boulder, which flows through Boulder, was also a favorite in its lowest 8 miles below the large springs the re-watered it and turned it into a very nice, somewhat large spring creek after it was de-watered just outside of Boulder by the irrigators each summer.
Thank you for reminding me how great the trout fishing was in some of the lessor (or hardly known outside of the locals) rivers in Montana.