The exception to the rule among low-cost carriers is US Airways. Because the Dividend Miles program was developed before US Airways transformed itself into a discounter, it is comparable in most respects to the programs of full-service airlines. In particular, Dividend Miles members can earn miles with more than 100 partner companies—far more than participate in the program of any other low-cost carrier.
The flip side of earning opportunities is redemption opportunities. Together they account for most of what makes a program worth investing time and energy in, or not.
As with earning miles, the general rule governing award options is that larger programs offer their members more choices than smaller programs.
Continental, Delta and Northwest members fare especially well on the awards front—domestic awards in particular—because these carriers are all members of the SkyTeam airline alliance. That means that they co-participate in each other's mileage programs, allowing members of Delta's program, for example, to redeem miles for flights on Continental and Northwest.
With award seats in notoriously short supply, such expanded opportunities can make the difference between snagging an award ticket and being forced to redeem twice as many miles for an unrestricted award, or staying home altogether.
For the majority of program participants, earning miles and redeeming them for awards are the primary concerns. But for truly frequent flyers, earning miles is a given and free flights aren't the principal goal. Bona fide road warriors participate in mileage programs to obtain the perks associated with elite status. And the elite benefit that trumps all others is upgrades.
Airline programs that feature elite upgrades fall into two camps. American and United offer their elite members unlimited complimentary upgrades only from unrestricted fares (e.g. from the highest-priced tickets). Continental, Delta, and Northwest, on the other hand, allow their elite members to upgrade from any published fare. Unless you're a traveler who routinely flies on unrestricted tickets, the latter policy is likely to result in more seat time in first class than the former policy.
The discount airlines' programs rarely feature elite upgrades because they lack either first-class cabins, elite program tiers, or both. The notable exception, as with earning partners, is US Airways' Dividend Miles program. Most US Airways flights have both first- and coach-class cabins, and Dividend Miles elite members receive unlimited space-available upgrades when traveling within the continental U.S.
Because frequent flyer program members have wildly different travel and purchase behavior, no mileage program is one-size-fits-all. But there is almost certainly a program whose particular strengths best dovetail with your individual requirements. Find it, stick with it, and reap the rewards.