PCB/SA
I can't pick both... I guess I'll go for SA, 'cos the Neutral album (darkness) really made it shine for me.
Now whenever I play that game I find myself humming all the way through.
SWR/SA are closely tied, but I picked SA only because I enjoyed the Darkness Album more than the SWR Orchestral one.
Please, PLEASE, don't ever use arrange albums to help you choose one over the other. They're not originals, and therefore not ZUN's music. Anyone with great musical talent could make an awesome arrange of a terrible song.
Keeping this in mind, I chose PCB because I really liked the music in it overall. Most of the songs there are easily remembered by one mean or another, and I could to most of these songs many times and probably never get bored of it. It has many of my favourites such as The Fantastic Legend of Tohno, Phantom Ensemble, Border of Life, Ancient Temple, and many others. Also, it was a HUGE step compared to EoSD, which IMO was pretty bad in terms of instruments used.
MS had pretty good music as well. The are composed so well, it's a pity that they only exist in the PC-98 games. It's so nostalgic. I really love The Grimoire of Alice and Romantic Children though. Probably two of the best songs I've heard in the entire series.
MoF was also in the list because many of the songs are well composed that felt somewhat optimistic. Makes me feel positive and all. It also has one of my favourites, The Youkai Mountain ~ Mysterious Mountain. The instruments used were also well done. It also gave some old-fashioned folklore sense, but not in a nostalgic way.