I found some open source R-Tree implementations in C#, but none with documentation nor signs of being used by someone else than the developer.
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I know of none, but I would point out that libraries like this tend to:
Thus lack of activity in terms of commits for the library should not indicate that the library is dead, it may indicate it is very stable and solid. If the library is either easy to understand or targeted at a relatively sophisticated audience (as R-Tree usage currently is) then you may find little online dialogue about it.
Lack of download activity is somewhat worrying. Though you are using a fairly niche library on a platform not previously known for heavy GIS/spatial query work (though the changes in SQL Server 2008 may change that).
If you cannot find a Java library of appropriate activity it is unlikely you will find a c# one. If you find such a java one a direct (as opposed to idiomatic) port is unlikely to encouter problems.
The NetTopologySuite is a JTS port to C# and it contains a STRtree class which is a read-only R-Tree
According to this thread there is an R-Tree implementation as part of Perst: http://www.mcobject.com/perst_eval