I have a stash of stereo 3.5mm keystones that I bought to extend IR over cat6.

It occurred to me when grabbing a few IR emitters out of the closet today that they are mono 3.5mm connectors. If I wire all 3 wires (+ - S) on the keystone on each side of the cat6 run, will a mono emitter plugged into the keystone still work?

I do it all the time and it works fine

Yes.

Now for the part that the old guys don't want to see: the educational part.

Before there were three-conductor plugs and sockets, there were two-conductor plugs and sockets. The tip was the hot lead and the sleeve was the ground. Then someone figured out that they could make a third conductor by using part of the sleeve as a separate conductor. We then had tip, RING and sleeve.

This could be used for stereo, as in headphone connectors. Or it could be used for balanced signals, such as your description of + - S.

And all this was on 1/4" phone connectors, probably invented by Western Electric, an arm of Ma Bell. What you're talking about are mini phone plugs, mini plugs, 1/8" plugs, and 3.5mm plugs. And sockets. All those names are for the same thing. (If I ever knew, I've forgotten what the older terms were for 2.5mm plugs and sockets.)

Anyway... if you put a mono plug into a three-wire socket, the ring will short to the sleeve and the wiring will simply be hot and ground. In this case, no problem. If the socket had voltage, though, you could be shorting the voltage.

This is why when Freddy does it (what you describe) all the time, it works fine.