In no order whatosever except as they occur to me (and sort of trying to avoid the mention of some others already listed):
1. Milwaukee Country Club; like a little Merion, with a world-class locker room, a pro shop that is steps from the 10th tee and the 18th green. Just about perfect in every comfortable, usable sense...
2. Wawashkamo Golf Club (Mackinac Island, Michigan); this one is my favorite. It is, quite literally, a clubhouse from about 1910. It has 1910 wiring, it has 1910 magazines laying about. But it is a model of simple beauty for another era of golf. When you are done with your round, a horse-drawn carriage picks up you and your sticks. See also, for most of the same reasons, Wequetonsing GC in Harbor Springs MI.
3. Troon. Of all of the famed courses of the Open rota, I think this one is my favorite. Moreso than the R&A, which is like a mausoleum, moreso than Prestwick (which is really nice), moreso than Muirfield (which is so stuffy you'll feel like you need oxygen), moreso than Turnberry (which has fantastic facitlities for eating and drinking and sheltering but which isn't really a "clubhouse," and much moreso than Carnousite, where the muncipal 'clubhouse' has all the charm of Torrey Pines.
4. There are two new clubhouses that I like very much. They cannot compare, history-wise, to anything that we've mentioned here of course. Both in Michigan -- at Arcadia Bluffs and at Shepher's Hollow. If I were to commission a new clubhouse on vacant land next year, and there was an actual construction budget (thereby preventing the buidling of another Winged Foot, or Newport, or even a Sebonack or Bridge), those are two designs that I'd ask the architects to look at. Really pleasant, functional, attractive work.
5. For my last choice I think I'll add Oakmont, just because I always liked the concept. Big and rambly, with overnight rooms, and with the pro shop given its own space in a separate building. Like everything else about Oakmont, it is a kind of a perfect prototype, but done in its own way.