I've spent a lot of time (eating) in Portland, ME. I agree with the mentions of the lobster rolls at Cape Elizabeth (totally worth the drive) and spending some time at J's Oyster.
A little off the beaten path
Lolita - A new effort by the former owners of Bar Lola, a restaurant which consistently produced some of the most amazing food I've ever eaten.
http://www.lolita-portland.com/
The Corner Room - Casual and comfort foody. This is one part of "The Rooms" restaurants in Portland. All three are worth checking out.
http://www.thecornerroomkitchenandbar.com/
Otto's is great for a quick slice of pizza
http://www.ottoportland.com/
Empire Chinese Kitchen and Bar - Totally worth checking out. Has great live music.
http://portlandempire.com/kitchen/
And you can't throw a rock without hitting a good cup of coffee. My favorite, Coffee By Design.
http://www.coffeebydesign.com/
Have fun! Portland is a great town.