I started by trying to 3D scan in the headphones stripped of the stock rubber in order to model the covers off of. Unfortunately, since they're black and shiny, they don't scan particularly well. So, nothing some time and calipers won't solve, right?
Once that was done, it was on to model what they'll actually look like. I based the design off of some jogging headphones I liked the fit of. Again, being buddies with your calipers comes in handy!
Then I used the two 3D models to make the positive and negative parts of the mold, and of course printed them out. If you use SolidWorks like I do, this tutorial could really come in handy if you've never used a part to make a mold before (http://learnsolidworks.com/solidworks_features/how-to-draw-a-coke-bottle-mold-in-solidworks). YouTube is super helpful in this regard as well!
Next, I just mixed up a little cornstarch in with silicone (maybe 5:1 silicone to cornstarch), filled up the molds (a vacuum degassing camber would've been nice at this point, but I didn't get much in the way of bubbles. So it worked out okay!) and waited about 20 minutes for the silicone to set up.
Then it was just a matter of carefully pulling the two halves apart, and trimming off the excess silicone. Since this type of silicone produces acetic acid as it cures, it's probably a good idea to wait a bit after they're trimmed up, and wash them a few times before sticking them in your ears for extended periods of time. But it smelled like it was totally done doing its thing by the following morning, so definitely not too long of a wait time!