If we're looking at western release only, I'd want:
1)Shining Force 3 Scenario 1
- best SRPG of all time. Only scenario 1 is *officially* in English
2)Panzer Dragoon Saga
- one of the best RPG battle systems ever
3)Fighters Megamix
- the most joyfully crazy fighting game I've ever played
4)Story of Thor 2 (Legend of Oasis)
5)Mystaria Realms of Lore
- criminally underlooked SRPG
6)Shining the Holy Ark
- fun first person JRPG with a fantastic soundtrack
7)Nights into Dreams
8)Burning Rangers
9)Virtual ON
10)Panzer Dragoon Zwei
11)Dragon Force
12)Guardian Heroes
13)X-Men Children of the Atom
- still my fave capcom fighter ever
14)Saturn Bomberman
15)Dark Savior
16)Night Warriors: Darkstalkers' Revenge
17)Shining Wisdom
18)Soviet Strike
- much better then the psx release
19)Astal
20)Albert Odyssey
If not just looking at western release, you could add some of the excellent JP only shootemups like Batsugun, Kingdom Grand Prix, Battle Garegga, Hyper Duel, Thunder Force V, Soukyugurentai...
Then there's Street Fighter Zero 3, Taromaru, Shining Force 3 Scenario 2 & 3, Grandia, the D&D collection etc, etc.