Near Allagash (across the street) is Foundation and around the back of that building is Austin Street Brewing. There's another one in planning (Battery something I think, but not sure if it's open yet).
On the way downtown via Forest Ave is The Great Lost Bear (good beer annd great food - Almighty Cheesus mmm) and the Bier Cellar just down the street from there (decent beer store).
Now for the goodies. Shipyard is in the Old Port section and honestly, could be missed. A little hard to find is Novre Res...excellent bar with tons of Belgian choices. $3 Dewey's is ok, but I'd skip if time is limited. Also in Old Port is Liquid Riot, a brewery and distillery. They do half shots there, which is nice. Other options are Rising Tide, Oxbow Blending and Bottling Room.
Down at Thompson's Point (near the train station) you'll find Bissell Brothers (one of the best in the area) and Bunker Brewing.
Foul Mouth is across the bridge, but it's the only one out there so it really depends on time.
Here's a photo to give you an idea of the layout of Portland: