Engine thumps lightly while idling

I have a 2002 Mazda 626 that over the last several months has the habit, while idling, of the engine thumping and the car ever so slightly bouncing. Recently, I had to have the auto transmission overhauled and when the transmission shop tech drove with me during the diagnostic phase, the tech said that the thumping and slight bounce while idling were related to the greater transmission problem. However, since getting the car back this thumping has reappeared. I needed a tune up so I had that done including new plugs and for awhiile that seemed to have ended the thumping/bouncing problem. However, less than two months since the transmission overhaul and three weeks since the tune up the problem has returned. Its bugging me to say the least!