Some folks like going to Auburn on I95 then taking route 4, the shortest mileage, but this route has way too many intersections, is slow thru Auburn and seems more dangerous and almost always takes about the same time as I95 to Augusta or Waterville.
If you are going on to Augusta or Waterville, Skip the turnpike south of Portland and take 295 right through town (like you were going to Freeport). It's at least 15 mins faster and the tolls are cheaper.
I grew up just outside of Waterville (Oakland) we always went up through Norridgewock, Madison, Anson. There are no real shortcuts, but there are two cut-offs you can take. One in Norridgewock and the other Madison. They really just get around a couple lights which are handy if you're stuck behind slow drivers or trucks.