I have a 2006 Mazda 3 sedan, 2.3L, 120k miles, manual transmission.  My car runs great, other than an intermittent pulsing vibration at idle that’s been going on for two years (~10k miles).  Intermittent, meaning at some stops I feel a pulsing vibration, others it runs relatively smoothly.  If I bring the engine 200rpm above idle, it goes away every time.  There aren’t any driving conditions that specifically result in the vibration that I can tell - it occurs randomly even within the same trip.  It does seem to run a little smoother when the engine is cold, but resumes when the engine is warm.  My engine has no codes that I know of, and definitely no check engine light.

Over the past two years, I've had the following things completed.  Some of these replacements/actions slightly improved the vibrations, but they haven’t disappeared:   new ERG valve, throttle bodies cleaned twice, new exhaust manifold O2 sensor, new fuel pump, all 3 engine mounts, new purge solenoid, new MAF sensor, new air filter (now only has 4k on it), spark plugs gaps checked and they visually look great, and 3 concentrated doses of techron fuel injector cleaner. 

Could it be a failing PCV?  It's never been replaced and it’s about the only thing that I haven’t checked/replaced yet.  I don’t think it’s a vacuum leak due to the intermittent nature of the problem.

This vibration is driving me crazy because I’m an engineer and keep meticulous mechanical care of my vehicles.  I bought the car new, so I know its not idling correctly.  I’d like to keep my car for a few more years, so any help would be appreciated.