CLR also infringes Oracle's patents and the only reason why Oracle is not
likely to sue Microsoft is that Microsoft could do the same to Oracle.

See 
http://jonathanischwartz.wordpress.com/2010/03/09/good-artists-copy-great-artists-steal/

Mono - the open source implementation of .NET also has uncertain legal status.

I doubt it is possible to create runtime like JVM or CLR without patent
problems.

--
Mikhail

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