Racine & Laramie's in Old Town, San Diego. The owner, Jeff, is an awesome guy who rebuilt the store from ruins over 40 years ago and has been running it ever since. His son, Dave, is a walking cigar encyclopedia, and the employees know quite a bit about tobacco and tobacco accessories of all types.
The "lounge" isn't very large or exclusive, but the regulars are always glad to receive new friends into their midst, and are extremely welcoming. Prices are pretty good for California... either cheaper than most other places or within $.50 of them.
The store is made of dirt (authentic!) the pipe selection is decent, a great selection of pipe tobacco is there, and the humidor is pretty well stocked. Not as large or inclusive as some other places, but it carries some damn good sticks.
And on top of all that, they gave me a job. So yes, I'm a bit biased, BUT, I did come here to spend my money as a customer first, long before they ever gave me a job.