It seems to be fairly common that long running beloved series will have sucky ending. Nominate the episodes that ruined the series, made no sense, or were just plain bad.
My nominees are:
How I met your mother
Seinfeld
Enterprise (not exactly a beloved series but it was getting better in the fourth season and it was a crappy ending none the less)
Lost and The Sopranos are going to top the list as well.
If you were unfortunate enough to suffer through the entire Dome series then you know those two could, at best, be listed 2nd and 3rd.
Lost.
Northern Exposure. There wasn’t really a final episode. It just . . . stopped.
Kinda Like Deadwood.
What is it with Star Trek anyway? They take the most annoying characters from ST:NG and then cram them into other series.
With Voyager it was Diana and Barclay.
With DS9 it was Lwaxana Troi
With Enterprise it was Diana
I like Lost’s finale and think it is massively overly attacked. And I think Battlestar Galactica’s final episode is a masterpiece.
I hated X-files final original episode. And the final episode of the renewed series. Two terrible final episodes.
I would like to nominate a series finale that ruined another series. They should have offed Rusty in the final episode of “The Closer”.
I have to say that the final episode of MASH was less than satisfying for me. It aimed high and had some success, but Hawkeye’s delusion about the chicken didn’t seem to work well. And that was central to the entire episode and thus to the entire closure for the series.
No one’s mentioned Dexter yet, so I will.
10 posts and no one’s mentioned “Castle” yet ???
Absolute worst. Can’t even cut them slack for not knowing it would be the last until the last minute.
Friends.
Probably not a popular opinion, but my big issue is that it was extremely risk-averse. Putting Ross and Rachel back together at the last possible second was very predictable and not supported by the storyline leading up to it. I don’t usually engage in shipping, but Phoebe/Ross and Joey/Rachel made a lot more sense than a last-minute Ross/Rachel pairing.
Seinfeld. Hated it.
At the time, I thought the Lost finale was complete bunk, but I now think they did OK. There was just no way to tie up all those loose ends!!
It didn’t turn out to be the last episode but Assignment Earth on ST:TOS sort of was. Gene wasn’t sure if Star Trek would get a third Season so he used it as a chance to basically do a pilot for another show he wanted to do. The enterprise crew were completely superfluous to the episode and had it turned out to be the last episode it would have been a terrible way to go out.
St. Elsewhere
Sons of Anarchy
I think the St. Elsewhere ending was beyond brilliant. Those who are disturbed by it should put down their snowglobe and think a while. 
I also admire the ending of The Sopranos. Sheer brass balls clanging for eleven seconds.
SOA just plain sucked the story well dry its last season, and the deafening slurp that was the final episode was just more of the same.
You mean Deanna.
It wasn’t even an original premise within MASH. Hawkeye sees something and it causes deep psychological problems, the roots of which have to slowly drawn out, was the premise of at least three episodes:
#109: After commenting on and being agitated by the youthful ages of some of his patients, Hawkeye begins sleepwalking (and behaving and talking like a child while doing so) and having vivid nightmares of his childhood friends being injured.
#115: Hawkeye learns about an acquaintance of his - a mediocre doctor - who is doing very well for himself back in civilian life while Hawkeye is stuck in Korea. Hawkeye suffers severe psychosomatic back pain through the episode as a result.
#211: Hawkeye treats a soldier who arrives with his clothing drenched, having fallen into a watery ditch. This stirs a repressed childhood memory of Hawkeye being pushed into a lake by a friend and nearly drowning, leading Hawkeye to manifest sneezing and other psychosomatic symptoms.
At least in the final episode, the baby/chicken thing wasn’t tied to something from Hawkeye’s past. Crababble Cove must’ve been a nightmarish hellhole.
They made a conscious decision to make the ending about the characters, not the story. I respect that.