Most common things done
intake
exhaust (downpipe, midpipe, cat back, etc.)
Shifter bushings and short shifter
upgraded torque mount
better tires
Some people are also using manual boost controllers and fuel cut defenders to up the performance as there isn't a plug and play piggyback or standalone engine computer out there yet. CP-E is close with their but you have to hack apart your factory wiring harness.
Coming from a honda background you probably don't know some of the more reputable companies that make stuff for our cars.... I would check out places like custom performance engineering, corksport and cobb. We are all still eagerly waiting for cobb to release more goodies for us, but in the meantime corksport and cpe have quite a bit out. Do a google search for any of those companies and you'll hit their homepages. Also check out protege garage, i think they are one of the sponsors on this board, they are pretty spiffy.
As far as issues with the car, the first speed3s that went out had problems with one of the bolts in one of the engine mounts breaking, causing the engine to fall out of the car, but thats an issue that has been pretty much addressed. They aren't selling the cars with that issue anymore, the dealer will have fixed that for you already.
There are ONLY three bad things about this car.
1)Shifter is a little soft, this can be fixed
2)FWD + Torque =

3)It is way too easy to go WAY too fast and get into a lot of trouble
Aside from that, you made a great choice, enjoy the new car and get an intake on it ASAP!