On the other other (third?) hand, sometimes you want GPGPU which even in laptops can give some speedup, not to mention not having to debug it on large computer. With intel, you're out of luck there.
Read the ati support list before buying an still closed source driver board.
Nvidia may seem better because they only have close source drivers. Compare it with catalyst, and they are pretty much the same (except you will not get dual monitor easily with Nividia)
I have ATI cards in all my linux machines. They work /ok/, but it really seems like ATI only gives lipservice to being linux-friendly. After making promises for over a year about how big there commitment is, the improvement has been disappointing.
I suggest Intel because of the lower power consumption.