I know the one built into a new MBP is much higher resolution (although you have to use 3rd party software to capture at the higher resolution, unless iMovie '08 can capture at full resolution - hopefully the new Photobooth with Leopard will fix this).
However there is more to quality than resolution, the external iSights have a much nicer lens, and I would think its good bet that its color reproduction is better than that of the built in ones.