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Airline/Frequent flier recommendations

It's quite important that you choose a frequent flier program with careful consideration and stick with it– doing so will get you tons of perks. Generally, if you fly >25,000 miles in a given year, you meet the minimum rewards category in your airline's alliance.

United

A bunch of people are United members, as it has a hub at SFO, is generally one of the cheapest options, a member of a big alliance, and has a lot of U.S. flights. Importantly, it's partners with USAir and Lufthansa, along with some other smaller airlines. As a silver member, you get automatic economy plus seats with extra legroom (awesome especially on transcontinental flights), 2 free bags, automatic eligibility for upgrades to first class within the U.S., and special ticket lines and security lines at major airports.

Note that if you book a YCAL (state-negotiated) fare, as of 2012 you'll only get 125% (instead of the previous 150%) EQM (elite qualifying miles), which are good toward your elite status.

US Airways

Just pick United. U.S. Air's customer service is quite bad, they don't offer economy plus seating, they have a hub in Philly, and they don't have as many flights as United.

Delta

Although offering far fewer flights out of SFO than United, Delta seems to be the only civil way to get to Africa. (United flights are typically double red-eyes with 12+ hours of layover in between). If you plan on travelling to Africa on a semi-regular basis, Delta is a good way to go.

Their frequent flier program is not too bad. They have added Economy Plus equivalent seats, so that major strike against them is gone. One trip to South Africa is enough for Silver Elite status, which gets you priority boarding and upgrades.

American
Southwest
jetBlue

Their customer service is absolutely fantastic, and their points (mileage) program is very easy to use. Their fares are generally on par with or cheaper than United, and while they don't have multiple levels of upgrades that traditional airlines have, their customer service more than makes up for it. The planes are newer, the flight attendants are nicer, and every seat has a lot of legroom (getting the EMS [even more space] seats sometimes leaves even a 6'-tall person reaching far away for his or her laptop keyboard!). The terminal in JFK is also a great place to hang out, use free and fast Internet, and eat fresh food of all price levels.