omg I love most of the dungeons <3 but my top three are still easy to pick as they stood out the most to me~
But I can't pick out on particular favorite so despite using 1, 2 and 3 there is no particular order in my list.

1. Huakke Manor. Love both normal and hard mode
2. Brayflox's Longstop Hard mode...I love the last boss in it. It's a fun fight xD makes me sad people expect me to LB before big bomb to skip the phase. Sometimes I don't even if it makes them mad at me so I can at least enjoy the fight lol
3. Praetorium....has my most favorite fight. Ultima Part 1 before it becomes the boring version in the ring of fire lol it has such a cinematic feel to it xD

Imma go one step further and list my top 3 trials/Raids too!
This one is listed in order unlike the dungeon one :3

1. Garuda Hard Mode. Garuda is hands down my favorite battle. I wish the twisters actually moved though via animation and not just the lil feather that creates the tornado spawning in a different place. other than that I love Garuda and is prolly the only extreme primal I'll ever care to do whenever I happen across a learning party for her lol
2. THORNMARCH! Can't wait to do extreme sometime as well. It's such a chaotically fun battle xD
3. First Coil Turn 3. A lot of people hate this turn. I know it drops no loot but it's fun! I get the feeling of actually exploring the place. I really wish we could explore more. All people want to do is streamline rush to the end of every dungeon lol. Turn 3 could have been really epic if there was more to it....but I already found the platform jumping as we explored our way through quite entertaining x3