Say also why you like them!

I'll start

1) Pharos Sirius
To me, is a masterpiece! The epicness of music, the encounters mechanics (difficult but not impossible), the awesome bosses cutscenes and the overall feeling to being into that dungeon, makes me no dubt on which one is my own preferite!

2) The Lost City of Amdapor
Here, seems to run into something outside the time itself, feels also like time have stopped there. And the background music gets along with that feeling.

3) Haukke Manor
Exploring the manor, and the feelings of what happens when you open that door first time are quite unique, then any boss you encounter fits perfectly with the overall progression of exploring the manor.