I've looked through similar issues with p030x codes, but nothing quite matches my recent issue.

I drove my SSEi from Pittsburgh to Boston this past weekend. On the second day of the trip, I at one point opened it up, but around 3000rpm, heard audible knocking and immediately backed off, My CEL came on, the code a p0303, cylinder 3 misfire. I got off at the next exit, filled the tank with gas and put in some fuel system cleaner, and got back on the highway. The code did not return over the next 3 hours of highway driving, though I did not open the car up to full boost for fear that it would.

Once I was home, the code was tripped while the car was idling. It had been tripped prior to the day of driving as well, also at idle. I've noticed no other problems, the gas mileage was great during the trip (30+), and there'* no evidence of rough idle or hesitation. Prior to the first CEL trip, I had opened it up to WOT with no problems, but both times I did after, there was knocking.

Start with testing your coils. There'* a write up on how to do that in techinfo/testing. I suspect you have a bad coil or a bad plug wire. With a single cylinder misfire I would lean more towards a plug wire. concentrate on #3, that'* the front center cylinder.

Tested the plug wire and coil, both seemed to be fine (though I haven't tested the disparity between that coil and the others yet). Pulled the spark plug, it too seemed to be OK. It may still be the coil, I'm going to need to test all 3 of them...is it common that a bad coil will cause only one misfire?

it can, but more common is the wires leaking current when they wear out. change one with another and see if the problem moves to the other cyl. if it doesnt try swaping two of the coils around. when is the last time you changed plugs and wires?