Mine are setup by type (WPC, WPC95, and early electronic). Then within the types they are lined up by either theme or by game designer.
I have the Universal monster games side by side (Monster Bash and Creature From the Black Lagoon). Then Scared Stiff next to them.
Medieval Madness and Attack From Mars are side by side (same game designer & WPC95 games).
Twilight Zone and Addams Family Gold are side by side (same game designer and WPC games).
The John Popadiuk (game designer) games are grouped together (they include: Theatre of Magic, Cirqus Voltaire, Tales of the Arabian Nights and Star Wars EP1). Sorry but I sold the World Cup Soccer.
The Steve Ritchie games are grouped together by WPC and then SYS7 games. They include Star Trek TNG, Getaway and then Black Knight.
I have Black Knight, Solar Fire and Pharaoh group together. These are the original 'double level' Williams games. I sold Jungle Lord (did not like it).
I have only one Gottlieb now so it is by itself in the corner but I had the Gottlieb's grouped together when I had them. These were the 1980's multi-level games (Black Hole, Haunted House, Spirit and Krull). Now Black Hole is by itself.