I made my list (phew, took a while actually). I didn't fixate on a number but I came out on a top 20:
1. Ys III (PC Engine Redbook)
Well this is my top game soundtrack of all time and I don't think anything can ever better it. It has been about eight years since I first heard this soundtrack and it hasn't lost a tiny bit of its power. A majestic thunder that stands on the top of the mountain and smiles proudly at the rest of the list.
Mitsuda's somophore score remains my favorite. The nostalgia from the game has worn off and the synth on some tracks sounds a little outdated but the soundtrack still stands very strong on its own.
3. Ys IV Perfect Collection vol. 1
All three volumes are amazing in their own right but when it comes down to the best 'album' I have to give it to vol.1 because of it's great flow and overall funky flavour. One minus point is the Ys I rearranges on the beginning of the album which I always skip because I prefer those on the original Perfect Collection Ys.
4. Panzer Dragoon Orta
A wonderfull adventurous score which seems to get hardly any attention. Saori Kobayashi's unique panzer sound is the driving force here but the contributions from Yutaka Minobe blend in beautifully.
I love Sota Fujimori's 'neo cyber gamemusic' style. Yamane's tracks are a bit weaker but they hardly tear down the quality of the album.
6. Ys IV Perfect Collection vol. 3
Volume three rocks the hardest. I mean, this is Ys at it's most brutal. But it also the most epic tracks like 'Temple of the Sun' and 'Bronze District' as well as two fantastic ending themes. Ryo's swan song in vgm (till Wild Arms years and years later).
7. Chrono Trigger The Brink of Time
An inspiring take on Mitsuda's debut soundtrack. I really wanted to list Chrono Trigger but I hardly listen to it apart from the occasional moments of nostalgia. I still consider it one of the very best RPG scores though.
8. Ys IV Perfect Collection vol. 2
This one is more dark and somber compared to the rocking vol.3 and funky vol.1 but the arrangements are fantastic.
9. Final Fantasy XII
I never got into Sakimoto but after I played the game for a while I warmed up and I started appreciating his style more and more. I only wish I could have enjoyed the game more because I really loved the whole world of FFXII and the music really added to the feel of it. Even when listening to some of the tracks I tend to 'dream away' into the various locations.
10. Ys Perfect Collection
A landmark arrange album that I love to death and would never ever sell off, it's such a classic. The first disc is absolutely flawless. The whole thing just flows like water. The second disc is a mixed bag but it has 'Endless History', nuff said.
11. Magic Knight Rayearth
A quirky little rpg score from the Saturn. I think it's underrated but you have to like the sound I guess (it was done in part by the same man behind Panzer Dragoon Zwei).
12. Dirge of Cerberus -Final fantasy VII-
I never ever imagined this would become a favorite since I didn't care for it at all when I first heard. Only a few years when I looked deeper I found some of Hamauzu's best work here, in both the orchestral and electronic tracks.
13. Ys Book I & II (Redbook)
Ys I' arrangement on the Perfect Collection is superior but for Ys II this is the place to be. Tracks like 'Subterranean Canal' are timeless and I never tire of them.
14. Dracula Battle II
The best Battle album, period. It doesn't have the classic tunes from DBI but the powerfull arrangements blow the first one out of the water (yeah I said it).
15. Dracula X
Two classic Dracula scores on one album. The Genesis OST has more character in it's sound (I always found the PC Engine OST a bit too bright) but overall I like both equally.
16. Last Bible III soundtrack
An underground megaten gem that suprisingly saw an album release recently. I love it and it's the only SNES score I listen to nowadays.
I don't even know who the composer is but who cares. This is oldschool gamemusic to the max.
18. Splinter Cell: Chaos Theory
Perhaps a bit too dark for general listening but man, there is nothing like it in vgm.
19. Saga Frontier II
Couldn't leave Hamauzu's classic out.
20. Rom Cassette Disc In SUNSOFT
Ok, I had to list atleast something from the good old NES. Actually this disc really does deserve a spot. Sunsoft made the best music for the NES and this disc collects all the classics. But never mind that, Batman alone is reason enough to list this disc, well to be more precise: stage 1 of Batman. That's right 0:57 of playtime warrants the purchase of this album. ^_^
EDIT: I changed the rankings a bit (FFXII especially was a bit too high).