1 - Zelda: Majora Mask (N64, GCN) - Second coming of the Hero of time, (hope for a triology), dark and moody, link's negative view portraiting a chaotic world in decline in the brink of destruction.
2 - Tales Of Phantasia (SNES, PSone) - Awesome RPG, great playability, great soundtrack, breathtaking for it's time, beats the hell out of newer Tales.
3 - Final Fantasy 6 (SNES, PSone) - Awesome, great argument and soundtrack, avoids being cliché, beats the hell out of FF7 and the newer FF's.
4 - Zelda: Link's Awakening (GB, GBC) - Same reasons as MM, the end of a chapter, the relativity of reality, the truth behind the obvious, all that beggins has to end, even heroes.
5 - Chrono Trigger (SNES, PSone) - One of the best RPG's ever, be it in story, action, art realization and attention to detail.
Runner ups... Metroid Prime 1&2 (GCN), Ocarina Of Time (N64, GCN), Wind Waker (GCN), Perfect Dark (N64), Resident Evil 4 (GCN), Banjo Kazooie (N64), Conker's Bad Fur Day (N64, Xbox).