Teance is probably worth checking out, I've never been terribly thrilled by it, but that's probably just me. It's a nice looking shop though.
Red Blossom and Samovar are on my list of it would be nice to get to eventually. I've had a few samovar teas and they're nothing to write home about. Haven't tried Red Blossom yet.
SF has two of the small handful of Lupicia stores, that's worth checking out imo. The one in SF City Center is probably most likely to interest you. It's the biggest around. If you're there there's also Puripan Tea Garden. Korean tea store basically. Haven't tried any of their stuff yet, but they got my curiosity. It's on the same floor as Lupicia, just around the corner.
Imperial Tea I haven't been to in the ferry building yet. I've been to the one in Berkeley, also nothing special there imo.
Aroma Tea Shop (6th and Clement) is an interesting place, checked that place out last weekend while I was up there. Has a really gritty chinatown feeling to it. Fun place to try out tea. They'll have you try some blue people oolong and milk oolong, personally not a fan of either. Try whatever you like though.
Japanese tea garden, as they mentioned is not a spectacular place for the tea, but quite beautiful. Sakura are in bloom right now, absolutely stunning. I didn't mind paying 4 dollars for a pot of YMY sencha, it's really a setting/experience thing. Absolutely stunning with the sakura in bloom though.
White Crane Tea Co in J-Town if you want to see the smallest tea store you'll ever find. Some good stuff and the proprietor is a great guy. There's also a few stores worth poking around in Jtown if you want to look for some nice teaware.
Asakichi in Jtown and the tea stand in front of it are worth poking into if you want some Koyamaen or Ippodo tea.