My wife has a 2009 yaris just hit 102k miles. It's a manuel transmission hatch back. What sort of maintenance should be done to ensure it runs well. I changed out the air filter. The car drives well. No noises or vibrations.
I have an 08, I changed out the manual trans fluid simply for preventative maintenance. To be honest though, mine has been pretty bulletproof. Toyota's really are made for people who don't like to do a lot of maintenance on their cars. I drive the heck out of mine and she just keeps going. Just hit 190k. Might want to think about doing a cooling system flush possibly given the year of it.
Just follow the owner's manual's maintenance section. The maintenance would be pretty basic on such car so you should be fine. If you don't have a hard copy, you can access a pdf version of the owners manual and sometimes service through here.