Frankly, I've never found a shop that I was 100% happy with. I bought my first 2 road bikes at a big store (Landry's) and while they were OK and I had my knowledgeable husband with me, they didn't really ask what they needed to. Hence, I've had 4 bikes in 8 years. My mtb is too big for me (Belmont Wheelworks), but since I hardly ever use it, it's OK for the amount of riding i do.
My best experience was with Quad Cycles in Arlington, where I bought my Jamis. It's a small shop, but they seem to cater to all different types of riders. So friendly and no hard sell.
I don't recommend the shop I go to now (ATA)... they cater to racers and hard core people. While most "regular" people consider me hard core, I am not. If you want an expensive European bike, it's the place to go. They do sell Giants, but no other US brand. It's funny, some people love this shop, as evidenced by comments on the web, but others hate it. SheFly told me her husband won't even buy tubes there!
I am just glad my husband is very mechanically inclined and we have all of the tools at home.