I've got titles that move in and out of my top 5 depending upon which day it is (Grandia, Star Ocean 2, Lunar, Persona 4, Shadow Hearts, No More Heroes, Tales of Destiny, perhaps WA2) but nothing has ever challenged my number one dog, Panzer Dragoon Saga (PDS) was truly ahead of its time. 3D graphics on a system that was supposed to fail using them, 360 degrees of customization across multiple dragon mounts, strategic and twitch boss combat, epic breaking the evil empire story, amazing soundtrack and of course Maaya Sakamoto. The epilogue evokes memories of El Hazard OAV's close; in short damn near perfect like everything else.
Take an evolved rail combat system and place it in three dimensions. Use the oddball puck Saturn controller which so clearly evolved into that for the Dreamcast. World exploration, endearing characters, hidden objects, this game found means to work all of this in a title that is now nearing 15 years old. It's certainly not the longest of titles -- if you know what to do, everything can be beaten and unlocked in 20 hours, but all that shows is a game does not need to be 60+ Hours to qualify as great.