In no particular order, but these are most definitely my top 20:
1. Paper Mario: The Thousand-Year Door
2. Mario & Luigi: Superstar Saga
3. Mario & Luigi: Bowser's Inside Story
4. Fire Emblem: The Sacred Stones
5. Pokémon Ruby/Sapphire/Emerald
6. EarthBound
7. Mother 3
8. Golden Sun
9. The Last Story
10. Tales of Phantasia
11. Final Fantasy IV
12. Final Fantasy VI
13. Chrono Trigger
14. The World Ends With You
15. Dragon Quest V: Hand of the Heavenly Bride
16. Dragon Quest IX: Sentinels of the Starry Skies
17. Breath of Fire II
18. Mega Man Battle Network
19. Sonic Chronicles: The Dark Brotherhood
20. Star Wars: Knights of the Old Republic