Pier 39 at Fisherman's Wharf has a lot of touristy restraunts and shops but buried closer to the ocean, near the salty water taffy shop, is a little stand called Aunt Fanny's Hot Pretzels. The pretzels are indeed hot but also doughy, drowned in butter, salted to perfection (if you prefer) and complete when dipped in cheese sauce (think nacho cheese sauce, so nothing too fancy). The first bite convinces you that you have embarked on one rich pretzel eating experience.
I think I would frequent this place a lot should the brand ever decide to expand to Portland - maybe close to the waterfront?