Hey Paul,
If I had to choose a single anchorage in Maine as my favorite, it would probably be Mistake Island harbor, I just love that place... Especially if there is a big swell running, you hear the surf breaking in what seems just a stone's throw away. The holding seems a bit iffy there, certainly not as protected as the Mud Hole, but one can easily spend a couple of days exploring Mistake and Great Wass by foot, and a place like the Cow's Yard in a dink... And, that's not even counting Roque Island, and that beautiful anchorage off the passage in there that I know you've anchored up in...
One place I don't see on DDW's list that I'd suggest - if you are lucky with getting favorable conditions - is Monhegan Island... Definitely one of my Top 3 in all of Maine, I've always loved stopping there... It is a bit of a challenge to visit in a cruising boat, but I've always found the locals to be helpful in pointing out a vacant mooring, etc... I haven't been there in several years now, every time I stop it's gotten a bit more touristy of course, but still a very special place in my book...
Best regards,
Jon