K&L, Cask and D&M all have something to recommend them. Slightly further a field Blackwell's is worth a look. If you're looking for American stuff (bourbon, rye etc.) the Healthy Spirits (15th and Castro) has a good selection.
I might also suggest Costco. They have interesting small batch producers that they feature and it seems to change fairly frequently and are VERY well priced. My husband has discovered new whiskeys, ryes and bourbons this way!