The entire soundtrack is remarkably well-done. I was extremely impressed. I find myself listening to the soundtrack close to once/day, lately. That said, Three Stars is probably my favorite piece (and by extension the non-Act 2 act opener music, which sounds like a brief version of Three Stars and isn't featured in the soundtrack), though the arrangement (maybe that's not the right word, since it has a different meaning in music but...) confuses me. It could be that it's a mix of styles or something (romantic + modern soundtrack?). Regardless, it's emotionally evoking, and I enjoy it a lot.
I enjoyed the rest of the soundtrack immensely as well, but perhaps the next few favorites would be (in rough to no particular order) Parity, Red Velvet, Cloudland Swing, Jitter, Painful History, Aria de l'Etoile, and Innocence. It's honestly really hard to decide or rank. It was all well-done and matched the scenes perfectly, particularly the everyday BGMs, such as Student Council, Ease, Raindrops and Puddles, Concord...
Actually, the only one that I thought didn't really fit in was the nurse's theme. It sounded very urban/SimCity-ish. I was confused.
I've actually got Parity set as my android ringtone (part of Rin's total character, imo), with Spin as a second if I get bored of it.