If you plan on keeping the M past the base warranty, I HIGHLY recommend an extended warranty if you are getting any fun out of life driving your M3.
My E46 extended warranty paid for itself pretty quickly, and then some. The parts for the M, and the labor costs the dealer charges are pretty crazy. If you do the work yourself, the parts at wholesale, while expensive, are about 35% cheaper than what the dealer charges. For example, my water pump failed, which is pretty common on the E46M3 (plastic impeller). The dealer charged the warranty company $2000 to replace. The pump is $400 wholesale.
For me coilovers, more so the alignment and ride height, turned out to be the biggest warranty hassle. Not the headers, not the Brembos, not the CAI, not the aftermarket audio, not the larger radiator or electric fan, not the exhaust...
I had to get lawyers involved to get any warranty work done on the diff and rear subframe. Wheel bearings (which will fail if you track the car), tie rods, bushings, and control arms are yours to repair, and even the lawyer told me I would have no luck pushing that.
BTW the extended 7/100 through penske for my 09 E90 was $4K. That policy has better coverage than BMWs 6/100.