These three are from the original PS days, but were highly innovative in their design and gameplay.
The first is Parasite Eve, a combonation of Survival Horror and RPG. Combat was done in an active time, 3D battle system where you could manuever your character to avoid attacks and give yourself a better firing position.
The second is the sequel, basically updated the system so you no longer went into a 'battle' bubble with every encounter. Also gave more flexibility with firearms and PE (parasite energies) to allow for more fluid game play.
The final one is also from Squaresoft, though it wasn't considered a hit, even though design, game play and artistic style were all brillant. It was Vagrant Story. A third person, single player RPG that has been refered to as being Midieval-Gear Solid. Attacks could be chained together to do everything from drain enemies health to you, repair your weapon, do status effects, ect. On top of that there was an incredible involve weapon creation/maintenence system where you could combine different materials to create more powerful blades that would then be attached to different mounts and given augmentation stones to change what they had an affinity to. And if that wasn't cool enough, the more you used certain weapons against certain types of enemies, the more of an affinity the weapon would get for them, and the more damage it would do. While this may seem like ove micro managing it worked seemlessly. And a ready supply of workshops with universal storage boxes made switching out blades, spears, crossbows, axes, ect an easy task for the right situation.