If you continually use just one or a very few inputs over a period of time, try taking one of your source components that you use all the time and connecting it to one of the unused inputs. Let your ears tell you if there is a difference in sonics. Depending on the design of the gear, there might or might not be. Most of the time, it will sound "different".
As such, use the inputs that you normally would and worry about the others if & when you'll need them. They will "burn in" naturally over a period of time during normal use that way.
I had someone that i know call me up about this a few months back. They had hooked up their CD player into their DVD input rather than their CD input. Upon doing so, they found that their system sounded very different and wondered why. Going back and forth between the two inputs using the same player produced easily discerned results, hence their confusion.
The difference was that the DVD input had never been used. The reason why they originally changed inputs was that they had relocated the player and the interconnects they had were just a bit short to reach the "normal" CD input. As such, they plugged into the DVD input, which left them with enough slack should the player be moved a bit during normal use.
This person was using a lower grade surround sound receiver. To them, using this type of gear, the sonic differences in used vs unused inputs in sonics was quite audible. That's why i say that people should decide for themselves. Not only will this ease their mind one way or the other, it will help them to decide what is, and what isn't "urban legend". Sean