I don't think it means when a show gets terrible. It's a point where a show makes kind of a left turn away from it's original formula and into something different, and never recovers. Happy Days continued to be enjoyable after Fonzie jumped the sharks, but from that point on, the character could do ANYTHING. Whatever reality the show had was thrown over for crowd pleasing fantasy.
You could argue that Trek jumped when Frieberger took over, so for the audience of the time, that was Spock's Brain. The series was no longer jaunty fun, but an overly serious and operatic, less-consistently well written sci-fi series. As soon as Spock's grey matter was being passed around and he was telling McCoy how to put it back in, series credibility was trashed.
Other shows that jumped: M*A*S*H, Cheers, Dallas, SeaQuest, Get Smart, I dream of Jeannie, and so many more. It's that point when you say "after (such and such) happened, the show started heading in another direction." Like when they introduce a baby into the format. It doesn't necessarily mean the show suddenly got awful.
True. Strictly speaking one could argue that after TOS' first season it was never the same again, but that isn't to say it was bad.
I, too, tend to think of "jumping the shark" as the moment a show has just gone too far and never manages to win me back. Strictly speaking, though, that sort of thing tends to be more incremental as you hang in because you want to like the show but eventually reach a point you can't stomach or forgive anymore.
TOS never really did that for me. Although there were occasional episodes that failed to really win me over the series as a whole remained quite watchable.
As such, Trek as a franchise has never really jumped the shark.
This is debatable from an individual point of view rather than as an absolute.
I could argue that TAS had "jump the shark" moments because while there's a lot in TAS that I like there's also a lot I find disappointing, and that's taking into account the period and conditions when it was produced. For me the films "jumped" in TVH. The film was too much off the rails for me and the films never really got back on track even though there were still decent moments in them. Suffice to say I never cared for any of the TNG films.
It's tempting to say that TNG "jumped" in it's first or second season, but they really just took an unusually long time to get into their groove. Yeah, they had a few howlers in the first two seasons, but overall it did get better as it progressed, and some of my favourite stuff was in TNG's first two seasons. For me TNG started to jump in its forth and fifth seasons as blandness and formula began to cement in place and I wasn't finding it as engaging. That isn't to say there weren't still some quite watchable segments in the later seasons, but overall it just fell flat for me and I couldn't forgive it anymore. It's telling that I only have TNG's first four seasons in my Trek video collection.
I rather liked DS9 in the beginning, but rewatching it doesn't hold up as well overall as I once thought. Overall I like only a handful of episodes from the show. And I'm one of the few who bailed after the third season and never looked back. There was just something about how the show was written that just didn't appeal to me.
VOY and ENT "jumped" from the get-go for me as they never produced anything I could stomach or forgive. I thought they were terribly written and perpetuated everything I didn't like from TNG's latter seasons and nothing of what I did like.
So looking at it that way as far as I'm concerned the franchise "jumped the shark" sometime in TNG's fifth season. After that I never really felt the same about how Trek had developed.
Suffice to say this is still the case because I think ST09 jumped in with the sharks.
But this is all my individual perspective, of which I know I'm in the minority. Your own mileage may vary.