Just one I'd call worthy, and it's very worthy: Racine & Laramie, in Old Town. It's an excellent tobacconist in a faux-1800s theme that looks and feels genuinely old, with a wide range of pipes, a museum of antique pipes, friendly & knowledgeable staff, a huge cigar selection, and a place to sit and smoke.
You may hear recommendations in town for Captain Hunt. They have a few briars, some pipe tobacco, that's about it. It's mostly a cigar store. There's also a cigar store in the Gaslamp Quarter off downtown; I'd seen a few pipes there in the past, but when I was there a few years ago they didn't carry them any more.