The best I've played, in order of preference:
1. Kaneohe Klipper Golf Course, Marine Corps Base Hawaii. It's a fun course, and you can't beat the views. It won't offer much of a challenge though, even from the tips. But playing the 13th is worth the entire green fee all on its own. Conditioning was super
2. Eisenhower Golf Course (Blue), Air Force Academy. Nice test of golf with great views of the Rockies - and always in great condition.
3. Andrews AFB near DC. Andrews has three tracks, but the South is the best of the bunch. I might have ranked it higher if it didn't remind me of every course I play around home in southeastern VA.
4. Mamala Bay, Hickam AFB in Hawaii. The winds off Pearl Harbor make this much more difficult than it looks.
5. Sea 'N Air Golf Course, I had never heard of it until I went to Coronado Naval Base on business. Couldn't have been more impressed, despite bumpy greens (an abnormal condition, from what I heard).
6. Eisenhower Golf Course (Silver), Air Force Academy. More fun, in my opinion, than the much more championship ready blue course - but at 6500 yards in the mountains, it's basically pitch and putt.
Tracks I wouldn't rank near these ...
Eaglewood Golf Course, Langley AFB in VA. Not bad after Hurricane Isabel destroyed to the point of a required re-build, but still not worthy of ranking.
The Pines at Ft. Eustis, VA. Total garbage.
Tinker Golf Course, Tinker AFB in OK City. Wasn't bad; just not a lot of character and wasn't in good condition when I played it. Play it in the winter and hitting into the greens is like playing onto the hardwood floor at Chesapeake Arena.
Navy-Marine, Pearl Harbor. Good course. Played it when it was jam packed and hard as a brick, but a good test of golf. However, with Mamala Bay and Kaneohe so close, it couldn't compete.
Sunrise Vista, Nellis AFB outside Las Vegas. Worst military course I've ever played, bar none. Especially when you consider the alternative public courses nearby.