Well, he asked about brew pub cities. It got a bit twisted (by me and others) but in truth, it's hard to argue with Portland as far as brew pubs. Philly has plenty of them, but not like Portland.
That's true. Portland, ME is among the top brew pub cities in the country. In particular, two of the beer bars in Portland (Novare Res and Great Lost Bear) both often rank among the top 10 beer bars in the country in various magazines (by everyone from beer-centric sources like Beer Advocate, Barleycorn, and Malt Advocate to general foodie pubs like Gourmet).
In addition to being a great current city for beer, it's got some of the most historically important breweries in the country. The Geary's cofounders (who also founded Shipyard) were among the first to travel to Europe and bring microbrewing techniques to the US, and brought the first post-Prohibition crops of Fuggles and other hops to the US to make traditional hops varietals available for US brewers.
Allagash, Maine Beer Company, and other breweries in the city are among the tops in the nation.
For fans of minor trivia, there's another city out in the Oregon territory that was founded over 200 later and named after Portland (the two co-founders actually tossed a coin to decide whether to name it Portland or Boston). They have a pretty decent beer scene, too.
(More seriously, I always find it bizarre when west coasters consider "Portland" without further specification to mean Portland, OR; to someone from the northeast, that's as weird as thinking that "Sacramento" means Sacramento, Kentucky or "Boston" means Boston, Georgia).