Surprisingly enough, it is hard to find comfortable shoes here. I say surprising since San Diego is kind of an outdoorsy sort of town. Sole Comfort is one of the places other than REI or Nordstrom where you can find some comfortable shoes, and their selection far exceeds what you can find at the other retailers.
They stock all the major "comfortable shoe" brands, like Born, Birkenstock, Dansko, Simple etc. The staff is very attentive and polite. If you can't find what you are looking for, or for that matter, don't know exactly what you are looking for, they can make some good recommendations and suggestions. The back of the store has a small "sale" section and you can find some good deals here, although if you have a popular shoe size, you'll probably be out of luck when it comes to the sale.
Occasionally, they will have a coupon that appears in the flyers that are distributed around La Jolla, making any purchase there a pretty good deal.
The only drawback is that this store is located in the major thoroughfare of La Jolla, so it can be difficult getting here off the I-5, and parking sometimes can be tight.