Over at Ars Technica they've written an article titled "Microsoft suit over FAT patents could open OSS Pandora's Box" (http://lxer.com/module/newswire/ext_link.php?rid=116455).
They love their sensationalism over at Ars, that's for sure. Firstly, I don't believe there is a "Pandora's Box" to begin with. Microsoft would love us to think there was though.
This is all about Microsoft loosing out. They know there is a threat to their profits from Free and Open Source Software, so they try and discourage companies and businesses pursuing it by creating this overwhelming FUD aura around it.
No doubt, if Microsoft win this I see two things happening:
1) them using this win as 'proof' that Linux is dangerous and illegal. And that Microsoft themselves will possibly pursue you if you utilise it.
2) them using this as a testing ground against IBM. These two companies are at a stand-off with their respective patent portfolios and if Microsoft can win in one court against Linux then they can take this and bolster their attack on the big one, IBM. I wouldn't be surprised if IBM was very interested in this case.
Either way, its completely safe to use Linux. Microsoft is coming under increasingly intense scrutiny (especially from the EU) over its use of their market position and business tactics.
Give it 10 years and Microsoft will be another IBM, still big, but not dominant any more.