There are several things that can cause an engine to run rough intermittently. You didn't mention service and maintenance history, but if the spark plugs have not been changed in the past 60,000 miles, you may wish to have OEM spark plugs installed. You didn't mention if the engine just idles roughly or runs rough at higher RPM, but you may wish to check the condition of the air filter to make sure it is not clogged, check the black plastic snorkel between the air filter housing and the throttle body for cracks, check for vacuum leaks, check the coolant temperature sensor for the ECM, check the idle air control valve, and check the MAF sensor and O2 sensor operation. Also, you may wish to run a bottle of Chevron Techron or fuel injector cleaner from a Toyota dealer through the tank.
MotorsForum website is not affiliated with any of the manufacturers or service providers discussed here. All logos and trade names are the property of their respective owners.