Bringing this back from the dead...this was new to me so I had to let folks know about the axle issue.
There is truth to the replacement axles causing crappy idle, I just rectified it on my '07 Impreza.
The original inner boot tore at about 130K and starting flinging grease onto the cat, I figured it out after investigating the smell. It was a weekend and I needed a quick fix (commuter car), so the only axle that I could find on a Sunday was an aftermarket unit from Advance. Outwardly it looked like a correct match in size and there were no problems installing it, but as soon as it was put back together the rough idle started. I've done work on my own cars for 20+ years and have never seen anything like this, I chalked it up to coincidence since there was no logical reason that the axle would do this. I chased all kinds of things and drove myself nuts trying to figure it out...PCV, spark plugs, vacuum, EGR, stuck valves etc. but nothing helped.
After searching through multiple message boards I found a small mention of it but no one seemed to follow up on it as a legitimate thing. Since I had run out of options I gave it a shot and replaced the Advance unit with a Subaru used axle from a dismantler. Problem solved! Idle is back to normal and all is well again.
The Advance axle was fine at cruising/driving speed with no vibration, but apparently the tolerances were not as exact as the OEM piece. The only thing that I can think is that the axles act as additional dampers/mounts on our longitudinally-mounted engines (the main motor mounts are relatively small in my opinion), and any play in the axles/CV joints magnifies engine vibration. At any rate, if anyone comes across this particular problem it's well worth repairing your axles with OEM units. While they are quite pricey new from Subaru, they can be found used online for much less. I found mine for $85 delivered from a 50K-mile car so they are out there.