Are those two cards you are considering purchasing? I don't know if there's a Mobility 9600 XT availible (I'm fairly certain there isn't), so I'd have to say the ATI card here; ATI has been in the mobile graphics arena for over a decade, whereas NVidia is relatively new in the market, having only about 3 years' experience so far.
As for these claims about ATI cards being incompatable with Linux, I haven't been able to personally test this myself, but other people I know who've tried have managed to get their newer Radeon cards working under Linux with no problem; I suspect the incomapatability claim is just poison from the NVidia/Linux Fanboys; neither company would be stupid enough to not work hard against any incompatability issues.
Wake up, George Lucas... The Matrix has you...