Derf00

It sounds like either the EGR, 02 Sensors, or vaccuum switch (brass thing with vacuum hoses that is attached to thermostat housing). Emissions systems run in what's called a 'Closed-loop' setting until after the car warms up to a certain temp or for a specific amount of time. Once the sensors warm up they provide the feed-back 'Open-loop' communication needed to adjust the air/fuel mixture and timing.

Pull the codes, and check the check those components out. It wouldn't hurt to check all your vacuum lines to make sure there isn't a leak in one of them.