IP in Mono falls into several categories.
1. There is stuff covered by the ECMA/ISO standards. This is covered by the Microsoft Community Promise, which is legally binding. This stuff is safe from Microsoft.
2. There is a lot of .NET stuff that Microsoft has released under the Apache 2 license, which includes a patent pledge. If any of this stuff is implemented in Mono, it is safe.
3. There is stuff in .NET that is not covered by the standards, and has not been released by Microsoft under a license that includes a patent pledge. Mono has independent implementations of the interfaces of some of these things. There is no Microsoft patent pledge covering these parts, and Microsoft may have patents on their own implementations. These patents would cover specific methods used in the implementation, not the interface.
The risk from #3 is small. Most important, it is about the same as the risk if you use that functionality in a non-Mono system. For example, I believe that there is an XML parsing library included in category #3. If Microsoft has a patent covering some particular technique of implementing an XML parser, there is no reason to believe that the people who implemented Mono's XML handling are any more likely to have infringed it than the people who implemented Java's XML handling, or Ruby's XML handling, or Python's XML handling, and so on.
Also, most of the things in #3 are things specifically related to Windows programming, so you'll only find them in .NET programs that were written for Windows. If you are writing for Linux, you don't need those things. Even if you want your programs to run on both Windows and Linux, you can do that without using the category #3 stuff. For instance, instead of using WinForms, use GTK#.
If Microsoft did decide to sue someone over their patents that cover the category #3 items that aren't Windows-specific, it is doubtful they would go after Mono. Microsoft has done enough to support and encourage the development of Mono that they would have a big estoppel problem to surmount if they wanted to sue over Mono. It would make a lot more sense to sue over Java or Python, where they would not face the estoppel issues. Remember, as I noted earlier, the category #3 patents are as likely to be infringed by those as Mono.