Here are my Top10 other than Final Fantasy, don't mind the order since I treat them all pretty much equally.
1. Super Mario RPG (Yes, the great Square game that nobody seems to remember now) - SNES
2. Golden Sun - GBA
3. Castlevania Symphony of the Night (For me it's a RPG, say whatever you want
) - PSX/PSP
4. Kingdom Hearts 2 Final Mix+
5. Grandia 2 and 3 - PS2
6. Soma Bringer - DS
7. Pokemon Gold - GBC
8. Chrono Trigger - SNES/PSX/DS
9. Brave Story - PSP
10. Rogue Galaxy - PS2