Uh, some favorites off the top of my head and in no particular order.
Aside from those top five, my list is constantly changing depending on my mood.
1.The Longest Journey
2. Chrono Trigger
3. Mother 3
4. Metroid Prime 2: Echoes
5. Castlevania: Symphony of the Night
6. Beyond Good and Evil
7. Portal 2
8. Final Fantasy VI
9. Legend of Zelda: Link to the Past
10. Spyro 2: Ripto's Rage
There's tons of stuff this list is missing, like Aladdin for the SNES, Paper Mario: The Thousand Year Door, Ristar, Minecraft, Ape Escape, Megaman Legends 2, Zelda 2: Adventure of Link, etc.