In general, and this is weird, but I actually find that a lot of the ancient 1.90 quests have aged better than a lot of their 1.92 and 2.10 counterparts. There's a lot of, uh, tricksy stuff in some of those mid-2000s quests that just doesn't hold up. It's hard to suspend my disbelief playing old-style custom bosses when scripting exists now, for example. Or, like, C-Dawg I think used the phrase "designed to abuse a system that no longer exists" when describing Sabotage Dragoon -- I think that phrase could be expanded to include a lot of quests from that era. (For the record, I like SD and I think the general gameplay concepts are good enough that I think it'd hold up if it were redone with scripting in from the outset, but as-is, I think he's right.)
I guess to put it simply, stuff that gets by on the strength of dungeon design and overworld design and aesthetic choices has tended to age better than stuff where the focus is on What ZC Was Technically Capable of in 2005, I think.
When I played Demo Quest (the original one, by Phantom Menace), weirdly enough, I found that it had aged surprisingly well? It still feels fun and challenging -- granted you have to be into the Zelda 1 style of gameplay, but in terms of quests that have that gameplay it's one of the best.
Also, I'd probably second Revenge II. It's definitely one of those things that's of its time, but despite being of its time it still feels fun to play. I'd probably vouch for Power of Geduina/Time After, too. A lot of Wild Bill's old stuff sort of is in the same vein too -- I dunno if I'd go to bat for Ocarina of Power since it uses a lotta weird 1.90 gimmicks born from puzzle limitations (invisible walls!!! Everywhere!!!!!), but Fall uh de Honky Pig prolly counts as does what's in Conquest for Power. Probably DFW's stuff, too. Link in Cestria and <Insert Quest Title Here> are a couple of weirdly forgotten Dark Late 2.10 Era quests that probably qualify, too.
I haven't played Golvellius la Quete du Second, and Panoply of Calatia is still relatively new, but I'd bet those are probably going to age well, too. Of course, I could be off-base...
Depressing Donuts, too.
I don't wanna toot my own horn too hard, but I'm going to anyway that's what I was going for when I made that quest. I wanted to make something that didn't get by on engine trickery, but that was based on the design of the puzzles and cool design stuff and dungeon themes that'd hopefully stand the test of time. I dunno if I succeeded though!!! That's up to everyone else to do the deciding about!!!!!!!!
(Also, uh, I don't want to be too much of a stickler for details, but it's Depressive Donuts, although I prefer when people just call it "I Hate Mayonnaise 2". That's what I consider the main title, really, sort of like how most people say Zelda II and not necessarily Adventure of Link. (I don't know why I made the stylistic decision to put the subtitle front and center??? Was I stupid))