Many National Forest's allow where you can get to camping, ie if you can drive up a dirt road and find a spot, you can camp (pack-in/pack-out).
The problems you will have so many of the places you list, well, like Flathead, most of the land around it is private, state-park or reservation land. East of Flathead, up the Swan Valley you might be able to find some nice places.
Missoula and Dillon are mostly private. South and west of Missoula up towards Lolo has some nice places, north-west of Dillon is Beaverhead.
West Glacier has some nice places near by that are NF. We used to go south of there toward Hungry Horse a lot