I use a couple actually. I like going to Palo Alto Bicycles for larger things, its further away, but much bigger and has great people. Look for Jeff, he's a manager there and is awesome with customers.

Locally I use Cal Mar Bicycles, its near El Camino and San Tomas. It's a bit smaller, but awesome people and great for the small things like if I need something while on my commute to work.

These are really the only shops I use. Palo Alto bikes is actually a little cheaper than Cal Mar, but its somewhat inconvenient.

My friends use Sun Bikes if you're further north a bit near Milpitas/North SJ. They say it's pretty good but I haven't had any work there so I can't really comment.