I feel the question as phrased seems somehow biased.
We're not talking about exclusivity. For starters the simple fact that you have regular continuing characters in a familiar setting is already good continuity. There's nothing wrong with periodic references to something before, but the major push of the story is to address something new. Far too often, though, it feels like a story is cobbled together just for the sake of tie-in references.
At first viewing DS9's T&T was amusing. The second and third time it's, "Why did they bother to do this?" To show that they could and to have a tie-in episode. Comics and books do the same thing, tie-in to what we've already seen. TWoK was also a tie-in story albeit one that furthered the original story "Space Seed."
Sometimes it can be fun, but often I find it tiresome. DS9's "Crossover" was a decent revisit to the Mirror universe. After that I couldn't care less.
That's because DS9 Mirror Universe episodes sucked. The first one was OK, but the writers didn't have any good ideas for the continuation, they just used MU as an opportunity to have a silly camp fun episode with people dressing up and girl-on-girl action.

It had nothing to do with arc-iness. You could have listed a bunch of great storyarcs in DS9 and other Trek shows, but you choose one that sucked to make your point. You could as well name a bunch of bad standalone episodes. Or, maybe more to the point, a bunch of great episodes whose events were cheapened by the lack of any references to them later on. (Since we're started talking about DS9 -
Hard Time is a good example.)
I love a good standalone, but the only shows that really and fully support standalones 100% are shows like
The Twilight Zone, with stories that are truly separate and not connected in any way. But when you have the same main characters in every episode, there has to be
some continuity. See, for instance,
Homicide:LOTS, a cop show where most stories are standalone (though with a few arcs that spanned over few seasons, but not in every episode, more like one episode in 5), but the regular characters are the heart of the show: the focus was on the ways that they were affected by the cases, and the characters changed in important ways and had things happen to them, some of them died, had a stroke, committed a murder of a suspect, left police, went to jail... all as a result of the cases they were working on.
Now if there is very little continuity, when main character have all sorts of things happen to them and witness all sorts of things in a standalone, but never seem to be affected about it afterwards, it becomes tiresome and absurd after a while. You start wondering, why I am even watching these people if they are never going to change a bit, and if they don't even care what happened to them a week ago?
Now TOS, for the most part, made the format work, due to really interesting characters, but the lack of development was starting to show in season 2 and 3, and it would have even more if it had continued as a show. All those endings with the trio bantering and everyone laughing on the bridge were getting silly.