My top 5:
1. Metal Gear Solid - exceptional story, excellent gameplay, innovative in so many ways.
2. Chrono Trigger - RPG perfection, ambitious storytelling combined with great characters.
3. Shenmue - A truly unique gaming experience. At its release it was easily the most ambitious game that had ever been released.
4. Sonic 3 & Knuckles - Separated they are excellent games, together they equal platforming perfection.
5. Knights of the Old Republic - IMO the best RPG of the last generation, with intelligent writing, a wonderful story and characters that were developed in such a way that I actually felt bad going to the dark-side.
Honourable mentions:
Morrowind - Spent hundreds of hours in that world.
Super Mario RPG - Such a delightful RPG.
Soul Calibur - Was almost universally given perfect scores, was unbelievable for its time.
Super Mario World - An excellent platforming experience.
Final Fantasy VII - My first RPG experience, as my top five will testify this game was good enough to make me explore many others.