What makes a dungeon good are theme, combat, puzzles, exploration, story, boss and atmosphere.
My favorite dungeon, Hyrule Castle from Breath of the Wild, excels in six of these areas.
The theme is strong: cohesive, understandable, narratively-linked and a true setpiece.
The combat is challenging, sophisticated, varied and engaging. There are two mini-bosses, two Lynel fights, a plethora of difficult enemies inside, and challenging guardians outside.
The exploration is complicated, detailed, non-linear and surprising. There are a number of different rooms to discover, many different floors, a variety of entrances and traversal methods, and secrets abound.
The story is compelling, tragic, understandable and mysterious. There are diaries, intricate rooms with environmental details, and a clear history and importance to Hyrule's legacy.
The boss is engaging and very fun to fight. Assuming you've cleared the Divine Beasts, Calamity Ganon serves as a great test of the perfect parry and is an easy but rewarding challenge at the end of the game. Assuming you've cleared none of the Divine Beasts, the boss is a 10-phase behemoth of a fight that puts all other final gauntlets to shame.
The atmosphere is excellent, foreboading, ominous and epic. The music is a great rendition of the Dark Hyrule Castle theme, the visual presentation is terrifying and exhilirating, and their are goodies around every corner that add to this history (even more with DLC).
The puzzles are not very strong. There are some puzzles in the Lockup and the Library, and there are Korok puzzles throughout, but nothing as strong as Naboris or some of the shrines.
My least favorite dungeon is Midoro Palace.
The theme is weak: why is there a palace in this swamp? Who lives here? What is it for? How does it tie into the nearby Saria Town? Not a setpiece. And the Death Mountain lead-in leaves a bad taste in the mouth even before beginning the dungeon.
The combat is bad: no interesting enemies other than Guma and Wosu, not enough magic or sword skills to be fun, the item is boring.
There is one puzzle regarding the Handy Glove, but it is simple and boring.
The exploration isn't interesting: the dungeon is small and very linear, and there are few secrets.
The story isn't important at all.
The boss is terrible; not as bad as the Island Palace or the Palace on the Sea, but still not fun.
The atmosphere is bad and there is no indication that the dungeon is in a swamp. The blue is elegant but boring, the music is identical, the item and boss have nothing to do with the rest of the dungeon.
Theme and atmosphere can seem similar, but theme is the "overall" feel and atmosphere is "visuals and sound" with some story and vibe laced in.
These seven factors are the most important criteria when evaluating Zelda dungeons.