Well, the games are further separated from genre into developer. I kinda consider Capcom fighter to be a completely different animal from SNK fighter, and I have Capcom's 3D fighters right next to their 2D ones. It really depends on what your into how you'd implement it. For example, I consider Beat 'em Ups completely different from Fighters, so I have games like Guardian Heroes and Die Hard Arcade right in the middle of my fighters and shmups. Shmups then lead to Rail-Shooters, which then lead to FPSs, etc etc.
As for 'unique' games, they pretty much go with my 'rhythm' games, so I have Cosmic Smash right next to Space Channel 5.