The Sapphire Passage. I thought Crescent Moon Village was a great level, and that's the passage said level is in. I also quite liked the other levels there too, like the rather odd Fiery Cavern (it took me years to realise that this level was based on the saying 'hell freezes over') and Hotel Horror.
Toy Block Tower as a kid was my favorite and I still remember how it goes while not listening to it. It also features Hoggus the artist pig who follows you almost everywhere in Doodle Woods.
I voted for Ruby Passage as it has the most consistently strong set of levels. The Fiery Cavern is probably a highlight for many, me included, but the other levels in the Sapphire Passage don't have the strong refining level variation and ingenuity to them. Hotel Horror is neat distraction, but the individual rooms don't offer base level challenges. I really like level design that takes an idea and uses every inch of the level to explore that idea. This is also why I'm not big on the openness of the Topaz Passage.
I love horror theme levels so yes I have to say that Sapphire Passage is my favorite passage in the game and it's the one that I replay the most. Plus Catbat is awesome.