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I've actually had pretty good luck overall (and been surprised a few times!).

The two big ones that really stick out are Giants: Citizen Kabuto and Jedi Knight.

Seriously, I thought they would have aged pretty poorly. Giants still looks gorgeous with that funky color scheme, both bright and washed out at once. And has the same great varied gameplay and hilarious humor.

Jedi Knight I thought wouldn't stand up at all - the levels are massive and without the modern aids I had gotten used to (maps, markers and such) plus the visuals are a bit (A LOT!) blocky. And the game was notorious for some of the tough lightsaber boss fights...

... and yet it still totally hooked me. Never put the game down, never needed a break, played straight through and solved it.

I'm sure there are more, but these are the two that immediately came to mind when I saw the thread.

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I agree, Jedi Knight has held up pretty well, the level design just is really good and varied.
I actually played the first Dark forces game (from 1995!) for the first time a few months ago, and that's also still surprisingly enjoyable.
Regarding OP's question:
Star Trek: Starfleet academy was a bit like this for me...I really enjoyed that game back in the late 1990s/early 2000s.
Got it again here on Gog, and have to say, as a space combat game it's really extremely weak when you compare it to top titles like the Freespace games.
Didn't totally surprise me, and one can still have fun with that game, but its fundamental mediocrity is much more obvious to me now than it once was.