Easilly Secret of Mana, with Mario RPG a very close second. Tales of Symphonia is hovering pretty close as well, but I don't see anything touch those first two games anytime soon, even with all the graphical horsepower that is used these days.

Super Mario RPG is also one of my favorites, as is Chrono Trigger. CT was the game that essentially opened the gateway to RPGs for me, so it will always hold a special place in my gaming heart.

Skies of Arcadia

It's a hard question, I haven't played o lot them... But my vote goes to Fire Emblem: Path of Radiance (considering that Zelda and Monster Hunter Tri aren't RPG's).

Persona 3 Portable in an eternal fight with Final Fantasy X. A choice is not possible.

Suikoden 3

I loved the idea of the Trinity Site System and the fact that they pulled it off so well (though you played from 5 total perspectives, 3 being the main characters). Its a major shame Konami didnt continue with the idea (or others taking it over).

All 3 main characters were awesome in their own right. Tons of characters (most of whom got a decent bit of story), an awesome cast of villians (Yuber is a Pimp) and hell you get to play through the game from the eyes of Mr. Baddie Himself!

The story was fantastic and Suikoden 3 still holds my favorite video game intro of all time (it reminds of a motion picture trailer).

Betrayal at Krondor

dragon age origins, its the game that got me into rpgs.

if your counting moba games then its league of legends

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Final Fantasy VII, Xenogears and Terranigma are all notable mentions