5. Persona 3 FES (PS2)
Incredibly interesting to analyze how it heavily incorporates the theme of Death as well as the fear of Death into it's storylines and characters. Also helps that it's an incredibly solid RPG with great visuals, music, memorable characters and an awesome pantheon of Personae. I personally prefer it over 4.
4. The Legend of Zelda: Link to the Past (SNES)
One of the very first games I got seriously into, and the best Zelda game in my opinion (barely edging out OoT). Gorgeous SNES goodness in terms of music and visuals, incredible dungeon design, epic bosses, smooth controls and an incredibly satisfying ending combine to make an experience that was often imitated, but never surpassed.
3. Valkyrie Profile (PSX)
A hidden gem of a game from the PSX era, this game combines elements of platforming, dungeon crawling and turn based battles. The game is divided into Phases, and actions like dungeon delving or recruiting party members take a certain amount of time, so there's a certain amount of pressure in that regard (though you have way more than enough time to get all the essential stuff done). Seeing that the main character is a Valkyrie, your party members have to die before they can be recruited, and indeed the "recruitment" scenes tell the story of their (often tragic) deaths. It also has an incredibly awesome Golden Ending, as well as the events that lead to said ending (about the last fifth of the game or so is different) but the requirements to get it are so obscure that I have no idea how anyone is supposed to figure it out without a guide. Was recently ported to the PSP, so those who haven't experienced this classic in its original form can easily obtain it.
2. Final Fantasy 6/3 (SNES)
The BEST Final Fantasy (again in my opinion) and the game that got me seriously into RPG's. Awesome characters, great balance (glitches aside), incredible storytelling, Nobuo Uematsu's best musical score, and filled to the brim with unforgettable moments. Of course, this is all headed by one of the best villains in RPG history - Kefka. I think Gametrailers put it best in their retrospective of FF6 - "Kefka was not a supernatural being, or the collected sum of all evil, or a mind warping God from another planet, he was a man, albeit a twisted soul, who sought supreme power above all else. He wasn't a puppet to a higher power, or a victim seeking revenge, he was just an awful human being, and a wonderful bad guy."
1. Suikoden II (PSX)
My all time favorite RPG, and game in general. To me everything in this game is just about perfect - the battle mechanics, the characters, the music, the visuals... The only thing that isn't consistently excellent is the translation, which is easily forgiven. An incredible tale about war and how it divides people, benefits the opportunistic at the cost of their morality, and how so many are massacred simply for the sake of bloodlust and how the "lucky" survivors have to live with their trauma. The story includes themes of political intrigue, blind nationalism, duality between life and death, holding grudges, and the gray morality that comes with war. However, when it all comes down to it, the story is about three children and the war that tore them apart. I love this game and I cannot recommend it enough.