Final Fantasy III and V (The US Final Fantasy III in the US is actually Final Fantasy VI. There just wasn't a Final Fantasy V until after Final Fantasy VII had already released and FF became more mainstream)
Mother 1 and Mother 3 (Earthbound Zero and Earthbound 2). Mother 1 was released like 30 years later in the west, Mother 3 has never been localized.
like 90% of Ganbare Goemon (Legend of the Mystical Ninjas). The first SNES game is also horribly localized and for some dumb reason they removed the internal SRAM (saving without a password). Probably rental related or somthing. And this has peeved me for my entire life because Ganbare Goemon 2 is probably one of the best Platformers on the SNES, a platform already stacked with some of the best platformers in gaming, and we got the worst version of Ganbare Goemon 1. This was also ongoing as every release after N64 (ending with the DSI) was not localized
The Original Custom Robo on the N64 (And if you've never played the Gamecube Custom Robo you owe it to yourself to)