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There is a gigantic difference between the fact that you might accidentally be infringing and knowingly infringing.
Can you "knowingly infringe" when you don't know for sure? :-)
Everybody keeps claiming that Microsoft might have patents on parts of .NET. For that matter, they might have patents on parts of the Linux Kernel (http://yro.slashdot.org/article.pl?sid=04/11/18/1338228&tid=155).
So should we stop using the Linux kernel now? Microsoft might have patents on it!
The fact is that Mono does not knowlingly infringe any patents, because Microsoft hasn't listed any actual patents it has that are required to implement the ECMA standards. The only way to know for sure would be to do a patent search, which is expensive. Further, doing a patent search and finding anything could make you liable for treble damages in any patent infringement suit, so it's actually better to just not know. Don't blame me, blame the SNAFU patent/lawsuit practies of the USA.
The patent situation is nearly identical between Mono and Linux. Neither group knows anything for sure, by design (to avoid treble damages).
Until someone brings forth specific patents that Mono/Linux/Apache/etc. actually infringes, nothing can be done. And until that point, raising the "but Microsoft might have patents" FUD against Mono is only a waste of time.