I've done both the farmer's market and Alcatraz lately (last 2 years). Both are great! Be sure to get the audio tour at Alcatraz and spend some time in a cell (creepy but also enlightening). You can do both in one day easily. And while the farmer's market is the best I've ever gone to, Alcatraz is just so unique. I agree once is enough, but once is almost a required SF experience to me.
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