Buying a different exhaust manifold or "headers" is the best way to increase the velocity of the gases exiting you engine. That's why there are different designed headers. Larger exhaust piping helps of course, but like Nik said you will lose torque on the lower end. Perfect example are the headers designed for the Honda's.
Take a look at DC, APEXi and MUGEN. DC's most popular header is their 4-2-1, uses more good bends, but seems to taper off slighty at the collector. This is good for mid range torque, but doesn't help a whole lot on the top end where honda have most of their power. MUGEN uses a 4-1 design that has larger diameter piping, very few bends, and a large collector. The MUGEN 4-1 header is the best for top end power, but the comes with the sacrifice of the low and mid range torque. APEXi uses the 4-2-1 design which by far is the best for overall HP gains. Further more the the ports and bend are deburred and hand ported for optimal exhaust flow. APEX also uses slightly longer piping before they make the final bend to the collector which mean more midrange torque, with out sacraficing the top end.
Although we only have one or 2 headers to choose from with our MP3's, the market will develop and we will eventually see more. Has anyone looked into SR-Motorsports? They have an exhuast for the MP3 and P5. I will call them to see if the have one in their showroom so I can see it in person. I guess it all comes down to what kind of power you want. Mid range torque or peak HP. I'm more into torque.