When you install .NET 3.5 on your system, while the .NET CLR is the same and runs the same, there's some additional Properties and Methods that were added to the Base Class Libraries in order to make some 3.5 features like LINQ work as well as fix a few customer issues.
Daniel Moth has a very nice diagram explaining what "RedBits" and "GreenBits" mean.
"When we say red bits, those are Framework bits that exist in RTM today i.e. NetFx v2.0 and NetFx v3.0...When we say green bits, we mean brand new assemblies with brand new types in them. These are simply adding to the .NET Framework (not changing or removing) just like Fx 3.0 was simply adding to v2.0 without changing existing assemblies and without changing the CLR engine."
Krzysztof has a blog post about these new (kinda obscure) APIs and fortunately a nice FxCop Rule you can drop into your C:\Program Files\Microsoft Visual Studio 9.0\Team Tools\Static Analysis Tools\FxCop\Rules folder and you'll get a nice warning if you bump into one of these APIs. To be clear, they are not something you'll bump into in your regular life, but it's possible. Dan Moseley blogged about this from the MSBUILD point of view.
The situation you might get into would be that you'd develop on a Visual Studoi 2008 system with .NET 3.5 and targeted .NE T Framework 2.0 (but you have 2.0 SP1 with these new 2.0 methods), then you deploy to an older system that has only .NET 2.0 RTM (not Service Pack'ed). At this point you might get a MethodMissingException because that older system might not have the new method or property. Of course, you could just install the latest 2.0, but if you don't want to, then don't use the new methods/types/properties. Hence the optional FxCop Rule.
Krzysztof send me a text file with the list of new Properties and Methods and I wrote a little program to generate an HTML file that shows the additions (many are new overloads) and links them to MSDN help. I couldn't get to the exact method overloads so do make sure the parameters line up when you're reading the help.
http://www.hanselman.com/blog/content/binary/RedBitsChangesv2.html
NOTE: This is a different list from the original diff I did between 3.5 and 2.0. The original list was the differences between all of 2.0 and 3.5 and this list is JUST the BCL. Just the core.
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