Just found: PostgreSQL 8.0.2 released with patent fix. PostgreSQL has therefore received a new minor version in which a patented caching algorithm (arc) was replaced with a non-patented one (2Q). The interesting part: this is one of the patents that IBM has released for open source. And why did they switch anyway? Because IBM has released these patents for open source use, but not for commercial use - PostgreSQL, however, is under the BSD license, which explicitly allows completely free commercial use.
For PostgreSQL itself, this would not have been a problem: as long as it remains BSD, the use of the IBM patent would not have caused any problems. Only a later license change - such as when someone chooses BSD software as the basis for a commercial product - would have been excluded.
A nice example of how even liberally handled software patents cause problems. Because medium-sized companies that build commercial products on open source would have lost a previously available basis - solely due to the patented caching algorithm (efficient storage of and efficient access to data - so patentable according to Clements' idea).
In the case of PostgreSQL, it went smoothly: the patented algorithm is not faster or better than its non-patented counterpart. And for the software itself, nothing really world-shattering has changed. But this does not have to (and will not) always go so smoothly. In the field of audio processing and video processing, the patented minefields are much more extensive and therefore much more critical for free projects.
Okay, one might still argue that this would not have happened with a GPL license. But with a GPL license, certain forms of use as they already exist in PostgreSQL today (e.g., companies building special databases on PostgreSQL without making these special databases open source) are not possible. You can take a stand on this as you like - ideology aside - the PostgreSQL project has chosen the BSD license as its basis.
Even well-intentioned patent handling in the context of open source software would therefore be problematic. Exactly this is the reason why I am generally against software patents.