Intake manifold gasket - it's the right year for the bad gaskets.
Also clean the throttle body.
To disagree with Caretaker, if done -right-, you can do a full flush and fill on the radiator and transmission. On the transmission that involves cutting a coolant line to allow the old fluid to exit while you have someone pour in new fluid until it runs clean. (I've never done this.)
To do a full flush on a radiator WITHOUT harming anything, you'll need one of those 'flush' kits that Prestone sells, but you won't actually be cutting into the radiator hose. (although replacing the thermostat with an Aisin thermostat for a Toyota Matrix isn't a bad idea, along with the top hose)
Remove the radiator cap. Drain the radiator completely, close the drain. Pull the top radiator hose from the radiator, connect up a piece of garden hose with the above kit, and run the hose either into a bucket (if you plan to try to find a place to recycle it) or into the grass. There's nothing in the stuff that'll cause a problem for grass, you just don't want animals trying to drink it. Fill the radiator with distilled water, _leave the cap off_. Turn on the heat in the car, start the engine, and let it run. Once fluid starts to run out of the hose, keep pouring distilled water into the radiator to keep it topped off (you may end up with some spilling out of the hose connector - you can try plugging that if you want). Once everything has run completely clean, shut off the engine. Reconnect the top hose, drain the radiator completely, and add concentrate. (you can also run the engine a bit longer while adding concentrate, because the engine capacity is larger than the radiator. Once you have put in the right amount of concentrate, you're done)
Then run the engine for another 10 minutes or so to blend the distilled water and concentrate.
If you don't have concentrate, you can use the premixed stuff instead, and just watch closely for the colour change.
That's a COMPLETE radiator flush without putting harsh chemicals into your engine, and makes sure you have only one kind of fluid. I've done this more than once. In fact, it's the only way I've ever changed the radiator fluid, rather than just topping off. You'll still have to clean out the overflow container.