The first Pokemon movie came out during the height of Pokemania, so I'd say they timed it perfectly. The Simpsons are the complete opposite, with the movie coming out years after the golden age ended.
I think the Spongebob movie was a few years too late, like 5 years after the show premiered. By the time it came out, I had lost interest. South Park was great timing, though; only 2 years after it started, and afaik still holds the Guinness World Record for most swear words in an animated film.
I feel like the SpongeBob movie releasing when it did probably helped the SpongeBob video game sales around that time. I recall SpongeBob SquarePants: Battle for Bikini Bottom and The SpongeBob SquarePants Movie doing pretty well
The original title was "South Park: All Hell Breaks Loose", but the MPAA wasn't comfortable releasing a movie with the word "hell" in it. So they renamed it as a subtle penis joke.
Stan Bush's tracks also are amazing. They feel dated now, but in the very best way, to me at least. Everything about Dare and The Touch is so much a time capsule of the era.
Way more amazing people are involved in that movie than one would think now.
Teenage Mutant Ninja Turtles. The movie debuted at the height of turtlemania in 1990 and became the highest grossing independent film ever at the time. It's also a genuinely good movie.
Technically not debut, but Sam Raimi’s Spider-Man was well timed.
It was shortly after the run of the 90s TV cartoon. VFX had just reached a point where convincing web slinging could be made. A few years earlier it would’ve looked awful.
I would also say that along with X-Men it started a new era of super hero movies where they could be taken seriously. Compare it to the Batman movies in the 90s, which are goofy in comparison.
Bit of a weird choice but maybe Dick Figures The Movie. It was based off of an animated YouTube series and if I recall correctly they got it out near the height of their relevance. It's not like the Angry Birds movie where it acted as more of a reminder that it was a thing than anything else.
Jimmy Neutron. Which is ironic because it was actually intended to come out part-way through the TV show, which is why the villains appear in a false redemption arc around the second season. It just feels weird in hindsight to think of any timing aside from what happened.