When replacing a circuit breaker in the service panel, how can I determine which neutral is associated with the hot wire?
Turn off all loads on the circuits in question.

Turn off the main for this panel. Possibly overcautious, but that's part of what's let me get old.

Either: short the dead circuit, or turn on an incandescent bulb on it (main off, circuit dead, still dead - just the bulb/fixture/lamp turned on.)

Pull neutrals and look for one with low resistance from the hot in question. There should be only one. Unshort the circuit or turn off the lamp and make sure the resistance changes (if nothing else is turned on, should be infinite, but if there are things that are not able to be switched off, may be non-infinite. But you should see a difference when you switch the incandescent lamp off or remove the short - it's a form of verification.

I think you have enough neutrals not to worry too much about this, but: beware of "Multi-Wire-Branch Circuits" where one neutral serves two hots. 

As for the wire colors, only white and green (with or without yellow stripe) are reserved (and IIRC, you can retag white to another color, but you can't retag green - and you can't retag anything else to white.) If your wiring is run in conduit, using the full range of available colors makes figuring out (what is connected to) the hot side of circuits much, much easier. Most household wiring is not run in conduit, so it's not often seen at home.