In the series Cabot Cove's exact location on the Maine coast was never fixed, and it tended to shift around according to the writers' whims, kind of like a modern day Brigadoon. The names of other Maine towns - some real, some made up - get tossed around with abandon. Although hints are sprinkled throughout the episodes set in Maine - a mention of how long it takes to drive to Portland, for instance, or the mileage between it and New York City - they seldom agree. Two episodes even briefly show sign posts grouping Cabot Cove with the names of several other real towns in Maine, but the sign posts contradict each other.
It should be remembered that these details were generated by people in living in California, not Maine, and as such they can't reasonably be used as a map. The exact location of Cabot Cove is, in the final analysis, a little continuity flaw that is best overlooked.
That being said ...
If one were to try to piece together the evidence, where in Maine would Cabot Cove most likely be?
(Click on the images to see them full-sized.)
Balancing Act: In Chapter 18 on page 261 of Martin Gottfried's authorized biography of Angela Lansbury, Balancing Act, it is stated that the producers based Cabot Cove on the real town of Castine, Maine. This is all well and good, but I've been to Castine, home of the Maine Maritime Academy, and this town, which has a very strong identity of its own, doesnt much resemble the Cabot Cove of Murder, She Wrote. It also is much smaller than Cabot Cove, with a population of 1343 according to the 2000 census.
Still, there is other compelling evidence to look at:
Penobscot Bay: In the episode "School for Murder" in Season 11, a nautical chart behind Mort's desk shows Penobscot Bay. Castine is located in eastern Penobscot Bay.
The Sign Post in Season 12: In the episode "What You Don't Know Can Kill You" from Season 12, Jessica and Seth's niece Amy visit the place where Amy's fiancÚ had a fatal (apparent) accident. As they head back to Amy's car, a road sign showing "Route 9" and "to US Route 1" is clearly seen, along with a sign post showing the distance to Cabot Cove and other Maine cities:
Somewhere Between Freeport and Brunswick
"The Szechuan Dragon" Sign Post: In the episode "The Szechuan Dragon" from Season 6, Captain Malachi gets dropped off just outside of Cabot Cove (never mind that everything is pointing in the wrong direction). A nearby sign post lists the distances to several real towns in southern Maine, and the place nearest the coast where the radii more-or-less converge is located between Freeport and Brunswick, Maine:
Distance from Boston: In the episode "Tough Guys Don't Die" from Season 1, Harry McGraw claims that Cabot Cove is 124 miles from Boston:
If you correct for the fact that the road isn't a straight line (unlike the one I drew on the map), then that distance works out to about the same place.
Down East Magazine: According to Down East Magazine's article "Where's Cabot Cove?" in the August 1999 issue, "Jessica Fletcher's hometown sure looked a lot like Mendocino, California ... even if it was meant to be Boothbay Harbor." They don't say specifically why they claim this, but it makes sense: Boothbay Harbor has similar characteristics to Cabot Cove, and a roughly similar population (2,334 in the 2000 census).
I think Down East has got it right, but decide for yourself: below are images of both Mendocino, California (Cabot Cove's stand-in) and Boothbay Harbor, Maine.
Boothbay Harbor, Maine