Lone Rider has started to make some decent brews. Improved on their consistency. They have a tap room out near the Angus Barn, but no food.
Big Boss has a good selection of beers at their taproom, no food. A few friends and I have had some negative experiences with the staff. Too cool for school kinda thing.
Natty Greenes pub in downtown Raleigh has a large selection of pub brews as well as other local beers. They also have a good pub menu with some beer pairings. Classic pub style.
Aviator has a taproom in Fuquay-Varina. I've tried their beers which are quite good but have yet to venture to their taproom to try their eats
The Roth Brewery (out near Lonerider off 70) is a small brewery (2bbl system) that is still working out the kinks. Very small taproom, kinda dark, no food. Minor issues with draft system leaving some beers somewhat flat.
check out NCBeer.org: North Carolina's beer guide.
for a complete listing of NC breweries and brewpubs