UA offers the most choice of flights from SFO, so unless you fly specific routes that other airlines offer better choices than UA does, UA is probably your best bet (as long as you stay elite enough to use the short checkin lines). If you stay with UA as your primary, AS makes a good backup to collect miles from odd AA, AS, CO, DL, and NW flights that you may occasionally fly.

AS may be worth checking out as your primary program if you do mostly west coast flying, particularly involving AS' hubs at PDX and SEA. As noted above, AS has many partners to collect mileage from as well.

If you fly a lot of short hops, would rather fly from OAK (that is closer to your stated location), and care only about free flights instead of elite perks, WN is worth a look.