Legend of Legaia, a game that as a kid took me several years to beat due to its difficulty. My favorite game of all time with a truly nostalgic ending.
Someone said KH: Chain of Memories...I can somewhat agree. I first played through it on the ps2 version because the GBA version to me was nearly unplayable. Its extremely tough game to get into. However once you figure out how sleights and character cards decimate the entire game(As Sora, but for Riku, its dueling bosses and is still overpowered and in your favor), its actually quite fun lol. Its still not for everyone..
Resident Evil 0 is another top 3 game of mine. I have many memories with close friends I used to have playing through the game, figuring out strategies with dropping keys and gear without an item box. The music was memorable like the opening, Progenitor fight, final boss. I'll always keep Billy and Rebecca as my more favorite RE characters, sadly with Billy MIA. Leech Hunter, even in recent years, I still discover new ways to tackle the 100 leech challenge. Top it all off, next to REmake which was my first RE game on gamecube, it was the very last classic Resident Evil game, something we'll probably never see again.