I have so many 64 controllers now that they are bleeding into other bins and such.
Interestingly, this is why my bins aren't labeled- I don't want to drive myself crazy constantly changing labels around (and I know I would).
I have a progression organization going on. Generic cables go in the bottom drawer, followed by gaming cables, specialty controllers, then my oldest system's controllers. The higher up you go, the newer the controllers get. That way if a console's controllers end up split across drawers (like the Xbox in my current setup), it technically doesn't mess up the system. Plus I can maximize space a little better.
Pre-Nintendo systems are the exception- all the cables & controllers for those are in a separate 3-drawer rolling cart. Since I tend to roll it into place to set up those consoles on the top of it, it's much more convenient. It also has a single Genesis controller in it- my Atari joysticks aren't the best right now, so... :p