<p>When I am working in .NET 2.0 projects with the newest version of ReSharper (4.1) I am getting warnings about using the var keyword and lambadas etc.. Any idea how I can disable this only for .NET 2.0 projects?</p>

You can actually use var in 2.0 projects.  It's syntactical sugar and the compiler works with it. Check out this for more info.
http://weblogs.asp.net/shahar/archive/2008/01/23/use-c-3-features-from-c-2-and-net-2-0-code.aspx