Old school RPGamer here, so allow me to give my top 10 favorites.
Honorable mention - Castlevania: SotN. Just remembered this classic as I was writing this but I didn't want to make this list an odd numbered list. So here it is, and it is a fantastic game.
#10 - Grandia 1. Graphics were meh, but the story, music and gameplay more than made up for it. Also, if I was savvy enough, I'd have Sue and Puffy doing an eternal "Rah-Rah Cheer" as my avatar. And I STILL haven't put in enough time in one game to master Feena's Time Gate move.
#9 - Final Fantasy Tactics. One of the only games I know of that uses the Zodiac sign system both in an intuitive battle design and in plot. That, and it has Ninjas and Samurais. I was happy. Great story, as well.
#8 - Secret of Mana. Pretty much the same as Grandia, except better. Although I wouldn't have minded the AI being able to use magic on the fly as well as I could, but that's just nit picking.
#7 - Breath of Fire 3 - Just an outstanding game overall, with some of the coolest transformations I've ever seen. Just wish it had Rudra from BoF 1 as a transformation. IMO, the best of the Breath of Fire series.
#6 - The Legend of Zelda: A Link to the Past. Great game overall. Still can't remember if I got 100% of the items in that game. Some of those hearts were tough to find.
#5 - Wild ARMs 1. One of my favorite storylines in all of gaming and the music suited the theme. I will never get tired of replaying this game every other month. The only downside is the in battle graphics. Still, an epic game.
#4 - Final Fantasy 3 (US version). So many characters and so many memorable moments in that game that this is the only Final Fantasy that I got emotionally attached to. So much so that if I were to have a daughter, her first and middle name will be Terra Branford. Pink esper FTW.
#3 & #2 (respectively) - LUNAR: SSSC & LUNAR 2: Eternal Blue Complete. Both of these masterpieces are awesome examples of what RPGs should be. For their time, damn near everything was perfect. The comedy in-game and in the out takes (especially if you tried to listen to the out takes prematurely) was also awesome.
However, my most favorite game of all time is...
#1 - Chrono Trigger. What more can be said of this game? It defines epic, and then defines everything beyond it. It is also the only game where I have the entire OST on my MP3 player.
Sorry about the lengthy post, but it's my first and I have a little bit of Mythbuster mantra in my veins. "If it's worth doing, it worth OVER doing."