I'd add the District Chophouse to the list (downtown brewpub), Dogfish also has a taphouse in Arlington or Falls Church I think, if that's closer (just a taphouse--they don't brew there). Brickskellar in Dupont has a big bottle list (although in my historical experience they are commonly out of 25-50% at any given time--haven't been in years though). Churchkey has an incredible tap and bottle list, but the crowds can be overwhelming--go early. There is a small beer garden in Columbia Heights called Wonderland Ballroom. I think there is a much bigger one somewhere in the NE part of the city, but I've never been. Brasserie Beck is a Belgian bistro with a REALLY good belgian selection, albeit a little pricey. There is also an English pub in Columbia Heights called CommonWealth Gastropub that is pretty good. I'm sure there are some other spots that are escaping me at the moment.
Edit: I think the Granville Moores mentioned above is the place I'm thinking of in NE (that I've never been to).