1. My Kitchen
2. Allagash
3. As of right now all remaining Maine breweries. I'm still trying to find a good third. To me all other Maine breweries seem to have the same characteristics. I'm not saying they are bad, I just haven't found one out of the bunch that sticks out as a third.
My favorite? Marshall Wharf Brewery in Belfast. A co-worker's father-in-law is the brewer there and they make some really great beers, including my favorite - the 11.2% ABV stout named "Chaos Chaos."
If you want non-commercial beer you'd have to try Liberal Cup in Hallowell. They brew their beer on site and can only get it in the restaurant. Good food too.