Technically you cannot modify anything that will affect the emission related function of the car, i.e. catalytic converters. So aftermarket headers are most definitely out, however a few people run the OEM european M3 or Z4M header and cat which will pass and provide slight gains.
Case in point: my car has an aftermarket x-pipe and mufflers (rogue / stromung) - all of which is bolted on AFTER anything SMOG related. It also has an Eventuri intake and tune. I took my car in for SMOG last month and although I passed the OBDII SMOG test, the technician said I failed visual for the modified intake. I swapped in the OEM box(temporarily) and received a pass.
Not all SMOG centers are as stringent as the next and many folks will pay more for a less discerning eye. It is also worth noting this only occurs every two years and some folks simply swap back to OEM for that short period of time.
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