A visit to Allagash and Bissell Bros is a must-say hi to Hester at Bissell, she's awesome. HIt up Foundation for Epiphany and Austin Street for some Brett based beers. On my next trip I will be going to Ebenezer's, but that's a few hours from Portland. If in Portland, visit Novare Res and King's Head for beer bars, maybe Great Lost Bear. Next to Great Lost Bear is Maine brewing supply, which has a nice selection of beer for sale too. A nice spot on the way up to Portland is Barrelled Souls-cool vibe and nice people.
Try J's seafood in Portland if you can get in. When Pigs Fly near Barrelled Souls is very nice for beer lovers and other people.
Go up to Freeport for Maine Brewing and outlet shopping (for the wife), LL Bean is there too. Don't go to Gritty McDuffs-shitty beer and shitty food.