I'm a fan of the Greene Leaf Cafe on Scotland Street. It's right across the street from William and Mary so it's decidedly a college bar but the draft selection is really good.
Dog Street Pub on Duke of Gloucester Street in Merchants Square may have the most interesting tap list in town, and it's decidedly not a college bar. Tap list is on their home page.
Bottle shops aren't a big thing there but The Cheese Shop, also in Merchants Square, has a wine shop downstairs that has an OK beer selection as well. The Wine Seller in Monticello Marketplace has a small but good selection and a small growler station. When I was there last week it was mostly Founders and Stone for growlers.
I haven't been to the new Alewerks taproom since they've remodeled but I do like what they make so it's on my list when I go visit my family again in June. They have a fantastic bourbon barrel porter, may be one of the best I've had. The bourbon is very restrained so it accents a great porter rather than punching you in hte face and making you forget about the beer.
had a favorite spot or a great bottle shop in the area.
-Pork