A few weeks ago, I noticed the car had developed a nasty knocking noise in the engine. It sounded to be deep in the engine near the back. You can hear the knock here and here. As it turned out, the problem was simply that the flex plate bolts, that hold the engine's crank shaft to the transmission's torque converter, were not as tight as they should be. The bolts has not backed out at all but one was finger tight and two others were just not very tight at all. The fourth one seemed ok.

I jacked up the car and took off the inspection plate on the front of the transmission (four 1/2" bolts). I then looked at the flex plate bolts (four 9/16") to see if they were tight. I had a can of white spray paint so I could paint the bolts after I tightened them so I would be sure to get all four. I used my wrench to short out the starter's solenoid to bump the engine over a few times so I could get all each bolt in turn. Don't forget to remove the wire that goes from the coil to the distributor so the engine won't start on you. It shouldn't anyway as the key is off but better safe than sorry. I got all the bolts tight and I also noticed that the lower starter bolt had backed out and was ready to fall out. I also tightened that one (5/8"). The car runs like a champ again!