Canuck,
Surprisingly, for an area that holds itself out as the triathlon capital, really there aren't any good tri stores that satisfy the needs of the very large triathlon community.
Ironically, the best place for nutritional products and basic gear is Orange Cycle. Orange is an all-purpose store, focusing mostly on road bike, mountains bikes and kids bikes. This is not known as a tri store. They do have a small amount of tri-bikes (litespeed, kestrel), and related products and tri-attire. If you want mutiple selections of supplements, GUs, bars, tubes, tires, etc., this is the place to go. They also have the best selection of clothing, including tri-attire.
Locomotion carries Cervelo and Felt. I like this store and the people that work there. The sponsor some really good triatletes in this town. They are light on product though. I have walked in looking for long-valve tubes, tires, misc. products, and they were out, so I went to Orange.
South Lake is a personal favorite b/c I like the owner Mark, who is the real deal - he is at the events every time helping out. He works harder than any other shop. His inventory is very small though.
Glory Cycles is the hot place for race bikes. They carry Orbea, Bianci, Ridley, etc. They have all the hot products. Most of the bike racers hang here. The owner is a super-nice former European pro. This is where I mostly shop. They do not carry nutritional product and are light on tri-stuff (though do carry Krestrel).
The track shack - the premier running store - has a very good array of nutritional product.
If you are looking for bike fit, skip the stores. Mostly of the competitive triathletes get fitted by Adam Baskin at PeakOneFitness.