For a multi-era collection, I like setting them up so they alternate between EMs (or early SS) and DMD machines. That way, the machines with speech and a lot of sounds (DMD/LCD) aren't right next to each other and you don't hear the other DMD machines while you are playing. It probably bugs people who like all the heads or playfield glasses to be at the same height, but I like it.
Kevin at Lyons Classic Pinball gave me the idea. Most his shop is set up that way generally. It's more of a PAPA-style arrangement IMO. If you play your way down a row, you cover several different eras of machines.
Pinball 2000s go on the end of a row nicely and tuck in out of the way.
I make sure all my EMs can be accessed from behind without moving the machines.