Alright then, we'll see how far I get with this before I run out of time for today.
Touhou 1 ~ Highly Responsive to Prayers
This is my favorite entry of the PC-98 era, musically speaking. It's notably different from proceeding material (particularly if you're listening to the original), but it's still composed of quality motifs and progression structures. Swordsman of a Distant Star (one of a few different titles for the track) is my particular favorite from the album; second place is more difficult to pick out, but I think I'll go with Eternal Shrine Maiden.
Touhou 2 ~ Story of Eastern Wonderland
This is where ZUN's definitive style was established, particularly with the distinction between stage themes and boss themes. Complete Darkness and Himorogi, Burn in Violet are my picks for this one, but with the corollary of ZUN's later SC-88Pro arrangement of the latter being the preferred version, both for instrumentation and slight arrangement distinction. Honorable mention to Hakurei ~ Oriental Wind.
Touhou 3 ~ Phantasmagoria of Dim. Dream
As my second favorite PC-98 entry, this one is more difficult to decide on. Nearly every track has noteworthy merit, and picking one or two immediately brings to mind the ones left behind. Nonetheless, I believe I'll settle on Eastern Mystical Love Consultation and Maple Dream..., with the former favoured toward the Untouched Scores version. Honorable mention to Strawberry Crisis!!, theme of my favorite character.
Touhou 4 ~ Lotus Land Story
While there's plenty of good pieces here, I have far less trouble deciding my favorites for this one. Sleeping Terror and Faint Dream ~ Inanimate Dream are far and away the best tracks in this era as a whole, and the latter remains one of my favorites in the entire series.
Touhou 5 ~ Mystic Square
All of the Alice-associated themes deserve recommendation, with Romantic Children and Grimoire of Alice particularly standing out to me. Additionally, I want to give honorable mention to Wondrous Romance ~ Mystic Square as an underrated menu theme.
Touhou 5 Music Room
A total of twelve bonus tracks were released with the final entry of this era, and I see no reason why not to consider this its own release. Anyway, it gives me an excuse to highlight Magic Shop of Raspberry and Phantasmagoria ~ Hardworking Day After Dark, as well as just generally draw attention to these oft overlooked tracks.
Alight, I'm out of time; be back later.