Speaking as someone with a hefty seven-figure total mileage balance (which doesn't compare to some on these boards, I think Randy has a nice eight-figure balance), my own preferences are as follows, in order:

Starwood: hotel rooms are almost always available, plus points transfer into most FF programs at 1:1 -- plus 5k bonus for transferring 20k. Starwood Amex becomes the best points-earning card to the extent that spending earns 1.25 miles per dollar on all spending when transferring points in 20k blocks to airlines with 1:1 ratio, which is better than the AA Mastercard for instance. Not to mention the card is cheaper.

American: I've never had any problems with availability. Partner awards are great. All miles earned count towards lifetime elite (we'll see if that lasts).

United: Availability on UA metal ain't what it used to be, but Star Alliance provides for amazing redemption options. Required mileage is low by most standards (e.g. 90k miles for a business class ticket to Australia from the U.S.). No fees for last minute bookings.

Alaska: Provides great availability. Only 10k miles to confirm an upgrade from any fare. Good partnerships (AA, BA, CX, QF, KL, CO, NW, DL for example). 20k domestic awards on AS metal.

Delta: Have had good experiences with availability. Good partnerships. But this is bottom on my list because I simply don't trust the program, award costs have risen, and I can always transfer points in from Membership Rewards so why go out of my way to earn when I have a monstrous MR balance?

(Oh, by the way, I'm not including Club Rewards or Membership Rewards on this list, perhaps I should and need to rethink my ordering. I'd probably rank Diners 2nd, Membership Rewards behind AA.)

I stay away from
USAirways: I burned my miles there. I know Randy has expressed some confidence over time. But what have I really lost by placing it safe and claiming awards? I've gotten use out of the miles, which is all I'd have gotten later anyway. And since they participate in Membership Rewards I can always deposit more if I need to. Current balance: 236

Continental: Continental availability is terrible. The only saving grace is that they have partners who offer better availability, like Delta and Alaska. Mileage prices are on the high side for valuable awards. Also a Membership Rewards participant, so why would I want to earn exclusively in the CO program? Exclusive earning, for me, goes to programs whose points are inherently valuable and where I have a more difficult time accumulating. Current balance: 719

Northwest: Love the elite program for domestic-only flyers, hate the redemption program. Massive price increases for awards. Saturday stays required for domestic standard awards. And I've found availability on NW metal to be pretty poor, at least as a non-elite there. If I ever want to claim an award on NW metal I'll transfer points to CO from Amex, or I'll use DL or AS miles. I use these miles when I can, keeping balance low. Current balance: 2719.

America West: They just lack the route network and partnerships to offer valuable awards. And while they offer some attractive fares, especially for last minute travel and for their premium cabin, I don't really want to fly HP anyway if I can avoid it. Current balance: 60.

I don't meaningfully participate in the Southwest, Airtran, or JetBlue programs either. Short expiration of credits and inability to redeem for the kind of awards that I value.

I have some BA miles but don't go out of my way to accumulate. I'm glad that I don't hold a big balance with Qantas, what with their gutting of their award chart.

I have plenty of points with Amtrak, Hilton, Priority Club, and a few others. I consider those somewhere in the middle of the pack. Amtrak transfers 1:1 into Continental and Midwest (big whoop, and they dropped bigtime in my book by pulling the rug out from under United transfers). Priority Club redemption is excellent in my limited experience. Hilton redemption is less excellent.