Bi-Rite, Tartine, Mama's, Bob's, San Tung, Tpumps, Mensho Ramen. It is a weird manifestation of SF group; many of those places aren't even that good. Peninsula and South Bay aren't much better, mediocre ramen places in particular draw huge lines (Santa Ramen, Santa Ramen, and especially average: Orenchi).
http://sanfranciscowaits.tumblr.com/