One problem related to engine noise has been reported for the 2004 Toyota Matrix. The most recently reported issues are listed below.
My 2004 Toyota Matrix xr with manual transmission has suddenly displayed severe mechanical noise from the engine/transmission area. Smog technicians wouldn't take liability to run engine for smog tests to register for the coming year, so is now registered as planned non-operation until I can get the car fixed. Googling "Toyota Matrix transmission noise" or "Toyota Matrix engine noise" leads to several sites in which too many owners are either experiencing complete engine loss due to "oil sludge problem" or total transmission loss due to "admitted transmission bearing design flaw". I will not drive this car again on the roadway due to the possibility of sudden and complete loss of transmission function at any time. This car is a great design for functionality, but I am totally dismayed and frustrated that at 120,000 miles, the car is off the road for serious engine and transmission flaws that appear to be very common, considering I bought Toyota for the reliability that we all know so much about. I have kept up on the oil changes since they were pre-purchased for 5 years when I bought the car, and have kept fresh after the 5 years expired. Very disappointed with the fate that this car has presented me, and the costs that I will have to incur to get it back on the road.