Wikipedia: Mono and Microsoft’s patents.
Mono’s implementation of those
components of the .NET stack not
submitted to the ECMA for
standardization has been the source of
patent violation concerns for much of
the life of the project. In
particular, discussion has taken place
about whether Microsoft could destroy
the Mono project through patent suits.
The base technologies submitted to the
ECMA, and therefore also the
Unix/GNOME-specific parts, may be
non-problematic. The concerns
primarily relate to technologies
developed by Microsoft on top of the
.NET Framework, such as ASP.NET,
ADO.NET and Windows Forms (see Non
standardized namespaces), i.e. parts
composing Mono’s Windows compatibility
stack. These technologies are today
not fully implemented in Mono and not
required for developing
Mono-applications. Richard Stallman of
the Free Software Foundation has
stated it may be "dangerous" to use
Mono because of the possible threat of
Microsoft patents. For this reason,
the FSF recommends that people avoid
creating software that depends on Mono
or C#.
On November 2, 2006, Microsoft and
Novell announced a joint agreement
whereby Microsoft agreed to not sue
Novell’s customers for patent
infringement. According to Mono
project leader Miguel de Icaza, this
agreement extends to Mono but only for
Novell developers and customers. It
was criticized by some members of the
free software community because it
violates the principles of giving
equal rights to all users of a
particular program (see Novell and
their Patent Agreement with Microsoft)
Edit:
I am not a lawyer, so I don't know how much software patent can be enforced, but Apple for example has licensed Amazon's 1-Click for iTunes. I found United States Patent 7162723 ASP.NET HTTP runtime, for example, I think describing general mechanism of ASP.NET. In there, there's a huge list of reference patents. There's also Systems and methods for a database engine in-process data provider, which covers ADO.NET.
Like I said, I'm not a lawyer, so I don't know how much of this would hold up in court, but my guess is they will have pretty good chance since unlike other software Mono is a direct imitation of .NET platform. Then again OSS has a long history ripping off of proprietary software's ideas like BSD, GNU, GNUStep, etc.
Much like the copyright and the music piracy issue, as long as we operate under the rule of law, we need to obey the law. If we don't agree with it, we need to tell the politicians and change the law. Richard Stallman thinks it's ok to rip off software ideas (I agree with him), but as a society we need to balance personal freedom and rewarding investors who has put in billions of dollars to come up with the idea. We have global warming and car companies to worry about in the US, so intellectual property issue is likely not going
to change anytime. So we are back to square one, living in fear of lawsuits.