according to rarity guide, rarest games I own by console (only including one's that appear on the first page when sorted by rarity)
GB - The Legend of Zelda: Link's Awakening
GBA - The Legend of Zelda: The Minish Cap
GBC - Pokemon Silver
GCN - Phantasy Star Online: Episode I & II Plus
N64 - Harvest Moon 64
NES - Little Samson
PS1 - Suikoden II
PS2 - Metal Gear Solid 3 Subsistance (Limited Edition)
SNES - Super Mario RPG
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