What I did was come up with a 'standard' for each system:
Video - 15khz with VGA socket
Audio - stereo with 3.5mm jack socket
Controls - IPAC-adaptor style, PS/2 mini-din socket
How you do this depends on each system, but Ultimarc do adaptors for a lot of this.  Dreamcast needs hacked VGA box & PSX adaptors (I have problems with mine, but others have got them to work with Ultimarc PS2 control adaptors).
Then I made a custom lead for each system which combine all of these things into one cable, terminated with a DB25 plug...these plug into a printer switchbox and then to the cabinets monitor, audio amp and IPAC.  This way everything (video, audio & controls) are switched at once, and other systems can be added with relative ease.
Something like this...
Console / PC:
Video Out         }
Audio Out         } Cable to input of switchbox
Controller input (IPAC Adaptor)   }
Cabinet:
Monitor      }
Audio Amp   } Cable to output of switchbox
Controls (IPAC)   }
The big advantage of using IPAC console adaptors is that you only need switch 5 connectors (PS/2) rather than all joystick/button inputs.
Oh, and I also actually switch a couple of other contacts which I use for the cabinets power button (requires a bit of console hacking).