M y favorites are, in this order:
"Akumajou Dracula X - Gekka No Yasokyoku" (a. k. a., "Castlevania - Symphony of the Night") for the Sega Saturn. Loved playing as Maria instead of just Alucard and Richter Belmont like on PS1. PS1 version held a better framerate and could do semi-transparent effects, but didn't have the graveyard and garden areas and, of course, no Maria.
"Super Mario RPG" for the Super Famicom. Wish I understood the dialogue better, but all-in-all it was a colorful, fast-paced RPG that didn't rely heavily on grinding for experience, seeing as the level cap was 30.
The original Final Fantasy for the FDS, and its remakes that added saving (outside of inns), better graphics and sound and most importantly MP as opposed to "X amount of spells before you had to go to an inn". Just a very simple RPG. All the elements are there.
"Monster Hunter Portable 3rd" for the PSP. Very slow to beat fully, but each main boss and enemies make sure every quest has its own reward, in the form of new areas or materials to make armor/weapons
"Golden Sun" for the GBA, and its immediate sequel. Colorful RPG, great story, nice mechanics, using special powers outside of battle to solve puzzles. Not really a lot of side stuff to do.
Anyway, those are my picks. Curious to hear yours. I'll take older ones as recommendations, seeing as my dad probably has them.