Off the top of my head (in the Hartford area):
104.1 changed from modern alternative rock to rap, then back (sort of). The problem now might be that modern rock has gotten whinier.
105.9 changed from classic rock to... I'm not sure. some late 80'ssome 90's, some 00's light rock, pop, worksafe stuff.
106.9 seemed to have an issue with the way modern rock was going, so they switched to classic rock-ish, but you only hear a few big hits from each classic band, plus stuff that's not really classic or rock. Sorry, Billy Idol, you will never be classic rock.
In Boston WMKK (Mike-FM, a Jack like station) was flipped to put WEEI (sports talk) on FM. But they did it too late. By the time WEEI jumped to FM, CBS's WBZ-FM (the Sports Hub) was over a couple years on the air. WEEI is just a joke now, where WBZ dominates the format.
Entercom should have done what CBS did with WBBM in Chicago when Merlin decided to flip (the second biggest national blunder after Free-FM) and put WEEI on FM prior to WBZ's startup.
Also in Boston, Clear Channel bought WFNX and attempted a "we play anything" format. It was too bland, but luckily they made up for that by starting the city's first EDM station. It's not too mainstream, but neither was WFNX as the frequency wasn't/isn't the strongest. However, it serves a niche listener core.
I don't live there anymore, but back in the day WHFS-FM (99.1) or "HFS" was an amazing alternative rock station. It was unusual in that it was one of the last large market stations not to have a pre-programmed playlist (the DJs actually got to pick the music) and was also organized an annual alternative "HFS-estival" music event.
In 1995 (per wiki) they switched to a "tropical Latin music" format. That switch was a an abject failure and to my knowledge 99.1 is now either a sports talk or all news format.
My opinion, the top two nationally within the last 15 years are: 1.) Infinity's (CBS) Free-FM, and 2.) Merlin Media's FM News format.
There are other local blunders that super cede these, such as anywhere CBS flipped back to a rock format (NYC's Free-FM going back to K-Rock), because CBS did a horrible job managing the format on the East Coast. So I think this should be separated into categories.
Many years ago WLOL 99.5 in the Twin Cities switched it format to Classic Rock in order to bring Howard Stern to town and compete directly with KQRS 92.5. Howard failed miserably here and the station switched to Classical music.
Personally I wasn't a fan two years ago with WLTE 102.9 switch from soft rock to country music.