i had exactly the same problem and it got worse, but then disappeared!
the problem occured about 9 months ago. On engine start up and switching off there was a loud clatter as if the engine mounts were loose, the clutch would vibrate and tap up against the bottom of my foot. This went away after one day and came back again a few weeks later when sitting in traffic, but this time i was having trouble putting the car into gear, i could only drive the car by starting it in gear.
So I immediatly took the car to my local garage, they had the car for 3 days running all kinds of diagnostics and testing but were no closer to identifying the exact problem although there was plenty of guessing, the clutch and flywheel was suggested, i was told the problem would get worse if it was. they called me on the 4th day to say the car was back to normal and to come and pick it up. the car appeared to magically cure itself overnight. i wasnt billed for any testing or diagnostics as nothing was found and no work was carried out. Had the problem about 3 months later but thought f*ck it and just carried on driving all day, the next morning the car was fine again.
Since my full service 2 months ago i havent had the problem again. I'd put my money on it being the oil change. I could usually sense when the problem was going to occur but I haven't had it since.