I think people have been expecting the Ys IV PC's to be reprinted since...1999, when they started doing the Falcom Millenium Series. They chose some good albums for reprints (JDK Band 1-w00t!), but I thought they could've done a lot better with their choices overall. Did anyone want to see Preprimer instead of the Ys IV PC's? Anyday now, Falcom...
(though seriously, they have the perfect excuse with Ys Origins coming out, so it may actually happen).
Ys III Perfect Collection is drastically different from the Duo redbook audio...It's actually less arranged and more like a standard OST version, with pretty good synth. Fun (and complete), but underwhelming. The Duo redbook is a much more dramatic and drastic arrangement overall and is one of the definitive Falcom "albums".
Ys 1 and 2 Perfect Collections differ from the original Duo redbook, but they're both more in the same ballpark. Both are that distinct 80's synth-rock of Falcom's by Yonemitsu, but they still differ from each other pretty good. Both versions are highly recommended.
Just a note: Both Duo redbooks mostly contain the "main" tracks, while more minor tracks are chip generated and you can't listen to them on the CD. Most level themes, boss themes and major themes are accounted for though (though no "Protectors", sadly). Also, some Duo tracks have the vocal parts included with the music. Minor issue, but it can be annoying in a few spots. The Ys Book 1 and 2 Redbook is worth it for the voice clips, in addition to the music, IMO.
Felghana Perfect Collection is interesting...It's technically not an arranged album. It's the OST for the game (which, in turn, is a bunch of killer arrangements of Ys 3's music), plus the Super Arrange (an arranged album of the Felghana OST, which is already itself an arrangement). So really, the OST's the same, but the OST's sound is much better than the gamerip that was floating around. Clearer sound and more fleshed out endings, so the gamerip is essentially obsolete now (really it was .ogg files taken from the game and converted, IIRC). Uh, the Super Arrange...Kinda turned out bad. This pretty much explains it:
http://www.rpgfan.com/soundtracks/ysfel-sav/index.html
Short story: Just get the OST.