1. Grand Theft Auto: Vice City
Still my favorite in the series.
2. Metal Gear Solid 3: Snake Eater
MGS4 tried hard to top it but fell short.
3. Shin Megami Tensei: Persona 4
4. SOCOM II: U.S. Navy SEALs
The only SOCOM game I ever beat.
5. Syphon Filter: The Omega Strain
A game truly ahead of its time. They should make another one of these now that PSN exists. But the franchise (much like SOCOM) has been booted over to the PSP.