+1 in most cases these days you can pass an emmisions test with a professional tune. We've taken some pretty extreme cars into inspection with our fingers crossed and passed. One guy even commented on how sick our car sounded. Supercharged/cammed/long tubes and no cats. He asked us to rev it up for him after we passed.
So it's all about making sure you tune those codes out. We sell everything you need to tune cars yourself but unless you know what your doing we recomend you get a tune done by a professional.