Well, this is the hardest question ever to answer, my favorites are:
-Deus Ex
-Fallout 2
-Strife
-Star Wars: KOTOR
-Super Mario RPG
-Chrono Trigger
Honorable mentions are:
-Eartbound
-Final Fantasy IX
-Dragon Quest VIII
-Xenoblade Chronicles 2
-Secret of Mana
"BONUS" Favorite unofficial modded game:
-Brutal HeXen RPG