I actually really like the flute effect melody.
Dense Woods B. It reminds me of a song by Aphex Twin called "Grass"
Barracks Settlement, Martian Underground, & the Dark Waters are all good too.
Flute room theme and Toriningen theme. The first time I heard the latter it freaked me the fuck out.
Dark Water and Dense Woods B are my top favorites. I also really like Mars (surface), Shield-Folk World, Mural World/Footprint Path, Number World, Kalimba, and Guillotine Room/Uboa.
Honestly most of the loops are pretty good, this game has some of the best short music I've ever heard.
I love every single track of the game. Yume nikki's soundtrack is one of the things that made me love the game so much. If I really had to chose, I'd go for the one that feels as one of the most iconic, the ending tune. It brings me chills each time I hear it.