MUD seems like the first place I think of when I think permaculture. They have a great site and offer a range of activities and workshops that are community oriented. The site is full of frugal ideas to live more self-sufficiently such as an amazing tool library, truck share program, and so much more. www.mudproject.org
The UM FLAT project is a University project led by students who are demonstrating sustainable living practices. They are relatively new, but are developing an outreach / education component, recently hosting a Terra Madre event. The site has a mandala shaped permaculture garden, a hot box for extending the season, chickens, a garage renovation that will be used as a community demonstration space, and quite a few other things. www.umt.edu/umflat
The PEAS farm has been increasingly using permaculture at their site. The barn is straw bale, they have a great root cellar with a living roof, they use a lot of reclaimed materials, their tractor runs on a single-tank vegetable oil system, they are experimenting in the fields a bit with companion planting, herb and veggie spirals, and for the most part, the farm is all student run and they run a great CSA and a lot of their food gets donated to the Poverello Center and the Food Bank. Awesome!
Sundog Ecovillage: Sundog has a world of potential and have made some good progress this past year. They have 40 acres in the Potomac and have been doing a lot of permaculture work. Last spring, they approved their permaculture plan for the core of their site that includes a community center, greenhouse, rocket mass heater, outdoor gathering space, new homes utilizing local materials, an expanded garden, innovative timber management practices, and host of other exciting plans. Check them out at www.sundogecovillage.org
Sage Mountain Center: is near Butte and they have several exciting building, garden, and appropriate technology features at their site. The have a few buildings that are made of cord wood, with cob, glass bottles, and other natural plasters. They have simple composting toilets, rain water collection, solar panels, passive solar structures, and they offer a yoga and retreat space for the local community. www.sagemountain.org
Missoula has a great resource for native plants. You can see their demonstration garden near the Kim Williams trail and Higgins Street, though I can't think of who the contact is.
I am sure there are many more, can anybody add to this list.