As I started reading this thread, Rock Creek CC was my first thought followed by Sun Valley and Clear Creek. Stone Eagle is an interesting choice because I never thought of it as a mountain course given its Martian landscape. Sun Valley (Trail Creek) started off as 9-hole Billy P. Bell creation and morphed into it's current form with the help of the RTJ clan. It would take an army of loggers to strip away the trees and clear the views, but under all that foliage is a really good, challenging (141 slope, tips), and fun course. Through the years the owners have always been skiers and tree huggers more than golfers, so its bones remain too hidden to be called a hidden gem. I'm sure the owners of the trophy homes around its edges wouldn't favor this sort of restoration.
My moderate travel experience has Rock Creek Cattle Company as the best mountain course. Perhaps its best feature is the variety of golf holes, with an amazing collection of "looks" off the tee. Also, despite the 400 foot elevation change, the walk, though long, is quite gentle.
I see Darius Oliver gave Rock Creek a 7. Man, Darius is a tough grader. Based on these ratings, you might conclude he is not a fan of hilly, mountain golf courses.
One thing I don't remember experiencing at Rock Creek is the "hillside" effect to putting, where playing on a hillside causes the player to lose perspective of what is level ground. On Stone Eagle, all of the putts break down the hillside more than it appears. I have heard that the Broadmoor resort courses in Colorado Springs have this hillside feature. If I were to place a further restriction on what constitutes a mountain golf course, I might add this hillside quality. Of course, this also happens at Riviera, where the putts regularly break uphill. I swear they do!
Does Grandfather G&CC count as a mountain course?