During the winter and on summer weekends, Gelandesprung Lodge (406/549-9777 or 800/728-2695, www.montanasnowbowl.com [1], $36 shared bath, $48 private bath), at Montana Snowbowl, offers reasonably priced rooms in a European-style slope-side lodge, with use the lodge’s hot tub and common kitchen.
Missoula [2] has several motel strips with plenty of inexpensive options. Most convenient to downtown and the university are the older places along East and West Broadway. The Highway 93 strip south of town offers more up-to-date lodgings but is farther from the center of things (unless your focus is the Bitterroot Valley [3]).
The City Center Motel (338 E. Broadway, 406/543-3193, $43 and up) has a decidedly budget ambience but is a fine place to stay, with in-room refrigerators and microwaves.
Links:
[1] http://www.montanasnowbowl.com
[2] http://www.moon.com/destinations/montana/missoula-and-northwestern-montana/missoula
[3] http://www.moon.com/destinations/montana/missoula-and-northwestern-montana/the-bitterroot-valley