The music really was the best part of Aquaria - it helped set the amazing atmosphere just really well. All of the songs pretty much fit the ambiance of the various areas too. I couldn't possibly gush enough about the music but that's preaching to the choir, so I'll try to list my favorites
1. Remains - Mithalos City - I love the aquaria main theme...and this is such a...well..haunting version of it. Totally fits the melancholy majesty of the city too, and the emotions you can imagine Naija feeling as she first sets eyes on the city. Nice, long intro, but when the music finally swells at 35-36 seconds in it's just too impressive. Gave me goosebumps the first time hearing it.
2. Arboreal - Kelp Forest - This was the first area I went to after open waters, in an attempt to find the surface - what a feeling it would be when I finally did - but arboreal is not for that. It's just a really upbeat tune that's at the same time kind of chill, it's just fun to listen to. Considering I was just starting to get the hang of controlling Naija and actually dodging enemy attacks, I had a lot of fun just controlling her in the environment to this tune.
3. Light - this is just such a peaceful, mellow tune. It's incredibly calming, and totally fits the innocence of the areas it plays in, starting out hearing this tune just set the mood right for the game, made me really just want to enjoy it. Also, it's more of the general Aquaria theme that's so solid. My favorite part is actually the ending when the more standard aquaria tune hits in, but softly. at around 1:15. So serene.
4. Open waters - It deserves to be on this list. It's, again, just a different tone of the standard Aquaria theme, but it works great. I was totally underestimating the game around the home waters, looking at the map and thinking "okay it's solid but not too large" and then I hit the open waters...and this theme greets me as well as a map impossibly large. It is, fittingly, just a more expansive version of the home waters aquaria theme, or it seems to be - a bit more echoing of a tune, hard to put into words, but it fit the feelings I saw when I opened my map and just saw it expanding into infinity and realized the game had so much more to give me than I was expecting.
5. Miniboss - It's just such an energetic, pumped up version of the aquaria theme. Totally gets me ready to go and fight things, but in that swift, agile way Naija controls. Not a frustrating theme either so if I got stuck on a boss the music helped keep me WANTING to fight instead of just getting frustrated and wanting it to be over already - more to the point fitting the music, my feelings of wanting the fight to end would be desperation as I got low on healing items/health! Which this sortof frantic theme fits that emotion, too.
It's really hard to rank songs. I'd like to also mention the song that plays after you've gotten Duo form and are tearing your way through the Body to get to the final boss. Such a well, this is an overused word, but epic song, really. Fit the mood so well of finally having power, and the means to fight back at that that's been tormenting Naija and Aquaria, and just totally decimating enemies that would've given you trouble before.