My game collection is everywhere.
The snes, nes, sms, and other cartridge cajoleries are stored in a trunk with the systems. I lost some of my genesis games during a move and deeply miss them.
The atari stuff is in random boxes I've yet to open in about ten years.
The Nintendo Wii collection is on the shelf near the main-room television (where the Wii is). Gamecube games are on one side, Wii games on the other. Games further left are the titles I play more often.
The PS1, PS2, and DS games are on the shelf with my dvds. Some of the PS1 games are on a CD rack near my computer. DS games are organized with stuff I'm more likely to play more often on the right of the line, with games I borrow from people on the furthest right. I don't think the PS1 games are organized.
The PS2 games were once shelved alphabetically, however have fallen into the timed and true 'stuff I beat on left, stuff I haven't beaten on right.' I try to keep series together, sometimes with a game from the series I haven't beaten on the right of the grouping.