I do not have a favorite "list" of items. I like many different dungeons for different reasons. However, if I were to mention one, it would be the single most underrated and misunderstood dungeon in the series.
The Temple of the Ocean King
Never before has a Zelda dungeon been as well implemented from a thematic, storyline or design perspective. What, indeed, can be told of the villain which isn't implicit in the conceptual design of his lair? The inexorability of its design - the very thing people were bothered by - is the greatest source of its strength. Each visit brings new stratagems to the table, and each change the play experience in significant ways. Completing the temple is a game unto itself, and by far one of the most worthwhile times I have had with a Zelda title. I would go so far as to say that the placement of pots* alone is proof of how well thought out the design is.
*Do you know how useful they are? Or how astute one's planning has to be to make full use of them?
One of the primary reasons I am so excited about Skyward Sword is that it promises to implement some of the greatest elements from that dungeon.