I have been cruising in and around Penboscot Bay for about a dozen summers and have already previously compiled my own list of likes based on where I have been. Penobscot Bay is less crowded than places farther south. If you venture past Schoodic to the real Down East, it is even more isolated.

Use this information for what it is worth, one sailor's opinion:

This is an attempt at a quick and dirty cruising guide for the Penobscot Bay through the Mount Desert Island area of the Maine Coast. I shouldn’t be doing this because one of the things I like about the area is there are relatively few boats, and there are lots of great places you can go where you will not see anyone else. So don’t come to Downeast Maine if you want to have all available amenities wherever you go, because most of the places I will list have no amenities. There is fog to contend with, cantankerous winds (though we usually do have good wind), and constant dodging of lobster pots – you can’t imagine the density of the pots until you see Jericho Bay at high lobster season. The weather is generally pretty cold even in the summer. I have been sailing out of Bayside (Northport) in upper West Penobscot Bay for 7 years. The places discussed are places I have been to and like. I tend to like the more isolated spots and the uninhabited islands so bear that in mind. I have not spent as much time in the MDI area due to time constraints so I can’t say a whole lot about the area but I do know a little. I list below the places I think are worth visiting. I don’t have time to give a lot of detail, so get out your charts and a cruising guide (best is – A Cruising Guide to the Maine Coast - Taft/Rindlaub) to learn more about the places mentioned.

Eggemoggin reach : definitely plan to sail the reach either east or west
Center Harbor: even if you don’t stop here, take a spin through the harbor, if you love beautiful boats, You will usually find a W class boat or two.
Wooden Boat School: Very nice harbor, room to anchor and moorings are available. highly recommended, visit the school store, tour the campus a fun stop if you are into wooden boats and how they are made.
Bucks Harbor: beautiful spot, excellent marina with showers, great place in bad weather
Horseshoe Cove: a personal favorite, if you go in, take your dink all the way back (check the tides), and see the reversing falls

East Penobscot Bay
Pond/Western Island: these islands are just outside the western entrance to Eggemoggin reach. Either one makes for a great lunch stop, or spend a day.
Pickering Island: Southeast of Hog island and west of Little Deer Isle. This has a great protected cove with room, good holding, swimming and nice place to land
Barred Islands: The ones just off Butter Island. One of the prettiest places you could ever anchor (and quieter than Merchants row, the other prettiest place).
Castine: a great little town, old money, few tourists, and over 4 centuries of history (learn a little something you may not have known about Paul Revere), excellent harbor. Explore up the Bagaduce river, and nearby Holbrook island preserve. Great hideaway anchorages inside Holbrook island and also in Smith Cove off Castine

West Penobscot Bay
Gilkey Harbor: a run from Pendleton Point at the southern end of Islesboro through to the ferry dock at the West entrance of Gilkey Harbor is the sailing equivalent of 12 mile drive (the cliff walk) in Newport RI. It is beautiful, and if you envy the very rich you will turn green. Pay very close attention to your charts(low water) but don’t be afraid there is enough water to get through for almost any sailboat even at low tide. Make a lunch stop at Warren Island off of the Islesboro ferry dock, this is a state park with a dock, campsites, and some state owned guest moorings.
Rockland: big town (by Maine standards), big harbor, great jumping off point. Great restaurants, all cruising needs available. This is a unique mixture of a working commercial harbor and has only recently acquired some “yachting overtones”. Good public dock. Great old fashioned main street.
Muscle Ridge channel (Tenants harbor to Owls head) this is a pretty area to sail through, if it is not foggy, don’t miss it on the way north. There are a lot of potential island stops.
Monhegan Island: This is not really part of Penobscot Bay but sort of guards the southwestern entrance. Monhegan is a unique and interesting island with great art, and great hiking trails. Its rocky outside coast has cliffs that rivals Acadia park for beauty and crashing waves. There is a reason it has been an artists colony for over a century.
Camden: Crowded and somewhat “touristy” for Maine, but there are good reasons, it may be the most beautiful harbor town anywhere. Nearby Rockport is almost as pretty, but is smaller, when Andre the seal was alive, Rockport was a don’t miss.
Seal Harbor: about 2 or 3 mile north of the ferry dock on the west side of Islesboro there is a nice little harbor with some interesting sights.
Turtlehead: the very northern tip of Islesboro is a conservation area with a nice half mile trail from the neck around the tip of the island and back, it is worth it to land.
Bayside: this is a very old and well preserved Victorian summer community with a lot of history, well worth a visit. There is a dock but no facilities for cruisers except water. A one mile walk will get you to a convenience store.
Belfast: A great Maine town and becoming a good harbor for cruisers, is a good harbor but rolly when the winds are southeast and east. Everything you might want is within 3 blocks of the dock.

North Haven/Vinalhaven area:
The Fox island thorofare is a must sail even if you don’t stop anywhere.
Hurricane Sound is also an exciting sail with loads of islands and ledges, watch your chart closely.
The Reach between Greens Island and Vinalhaven is a nice sail

Pulpit Harbor: This is a great harbor, there are lots of moorings to grab, or you can anchor. It is fun to sail into, but you won’t feel isolated. The Island Store is within walking (1 mile) distance. Some evenings the windjammers will serenade you with Amazing Grace on the bagpipes, others, young girls selling fresh tollhouse cookies will come around after dinner in a clumsily rowed inflatable.
North Haven the marina/boatyard (JL Browns?) is able to fulfill most cruising needs and rents moorings.
Perry Creek: grab an empty private mooring or anchor, take your dinghy exploring of to the head of the creek. This is a very beautiful spot, protected, with quiet waters. There will be other boats but you will feel more isolated than at Pulpit Harbor.
Winter Harbor & Seal Bay Both popular spots but I like them better than Pulpit Harbor which is also usually crowded. The Protection is excellent and you will see seals.
The Basin: not for the faint at heart and figure the tides if you go in, there is water in the Basin but the entrance is tough unless you go in at slack tide.
Hurricane island: this used to be a thriving community with hundreds of stone cutters living and working, very little trace left of the town, it is fun to walk the trails. Outward Bound used to maintain a couple of guest moorings. Great day stop.
Brimstone Island: this is basically just a big rock out into the Atlantic off Vinalhaven. It is a great place to stop and look around, There is an incredible cobblestone beach made up of black volcanic rocks.

Deer Isle & Isle au Haut
Isle au Haut Thorofare: there are cheap self serve rental moorings right off the town dock. This is barely a town, but that is what I like about it. Walk to the store, or hike the Acadia trails to Mt. Champlain or to Long Pond for a swim.
Duck Harbor: My favorite place, the harbor only has room for a handful of boats, so get there early. The best short hike in the world is from the harbor up to the top of Duck Harbor Mountain.
Merchants Row/Deer island thorofare: there are too many pretty islands here to enumerate. Take your pick of great places to anchor overnight. I like the little channel between McGlathery and Round Island. The area is another favorite of the windjammer fleet and in late afternoon you are likely to have one sail in to anchor nearby. Do not miss this area. One caveat, Lobstermen out of Stonington will “wake” very early in the morning on their way to their pots

Mount Desert Island area

You could spend a whole summer exploring Blue Hill bay, Jericho Bay and all around MDI.
Plan a sail up Somes Sound on MDI, the East Coasts only major fjord is a must, it is breathtaking. A great and very protected anchorage is at Valley cove near the outer end of the sound, take a hike up Flying Mountain for the view.

Both Northeast and Southwest Harbor, are great boat towns, especially if you like looking at Hinckley boats.
Lunts Harbor on Frenchboro is a must, I love it for its beauty and isolation, the harbor is a throwback to earlier times in Maine. There are great hiking trails around the island.
Swans Island/Burntcoat Harbor is a pretty working harbor
Places to go on my futures list:
Mount Desert Rock: both to see it, and hopefully to see whales ( I had a rare close encounter with a small whale who bumped my boat on purpose off Camden, and I want to see more (but not more contact)).
Matinicus, Criehaven (Ragged island), and Matinicus Rock.
Cranberry Islands
Blue Hill
Schoodic Point and beyond