Microsoft claims the Linux kernel and Open Office each violate over 40 MS patents, and Linux violates over 200 patents.
Open source software developers are prohibited from paying patent royalties by the terms of open source software licensing agreements. Some dispute whether algorithms are patentable, but the compression algorithms for GIF and MP3 are patented, and the patents have been enforced.
According to Technocrat.net (http://technocrat.net/d/2006/6/30/5032), litigating a single patent suit typically costs 2-5 million dollars, and companies can be sued for using software which violates patents.
On its patent policy page (http://www.novell.com/company/policies/patent/), Novell states "In reality, open source software poses no greater risk of patent infringement than does closed source software."
Trivial patents have been granted. Clearly, some of them are not inventions. For instance Amazon's patent of the one-click buy feature: (http://www.gnu.org/philosophy/amazon.html#whyBoycott).
The patent system was created to foster innovation. Much patented software was originally created as open source.
Open source companies are themselves acquiring patents to defend themselves with the threat of counter litigation against those who would sue them.
On April 2008 Red Hat filed a brief in federal court arguing for the limitation of software patents (http://www.press.redhat.com/2008/04/07/red-hat-asks-federal-court-to-limit-patents-on-software/).
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