Plundered from my STC post.
Just about anything Falcom released on it, their composers always got good sound out of it. I liked when they got up to Brandish 3, Legend of Heroes III and LOH IV, where they were basically doing epic RPG scores on it. The various remakes of both LOH scores totally pale in comparison to the PC-98 originals (not helped by Falcom's poor choice of samples). And of course, classic Ys and Sorcerian.
Yuzo Koshiro was always a fan of it, he redid a couple scores using PC-98 synth (Etrian Odyssey and one of the Metrovanias).
Other than the ones Falcom released, I don't think there was too much officially released PC-98 music. I'm more than happy to be proven wrong.