The Sand Temple is by far my favorite dungeon in Spirit Tracks. It reminded me of the Spirit Temple from Ocarina of Time in not only theme, but also heavy emphasis on puzzle. The Sand Rod is such a fun item to use and makes for some clever puzzles. Nintendo must have thought the same with its return in A Link Between Worlds.
The one thing I disliked about the dungeon is the boss. There was much frustration to be had for the catapulting of the final boulder into its side.