What are the best resources to read/learn about the internal details about the .NET CLR?
Without a doubt, "CLR via C#" by Jeffrey Richter for CLR v2 details, along with the CLR team blog for CLR v4 changes.
Apparently Richter is planning a new edition of CLR via C# which should ship in time for .NET 4.0.
I found CLR via C# very useful indeed - it covers lots of detailed stuff about what the CLR does from C# code examples.
As several other people pointed out CLR Via C# is a great book.
My personal favorite at #2 though is "Essential .Net" by Don Box and Chris Sells. This really dives deep into parts of the CLR not covered in other books and gos into detail about such items as interface method invocation.
I would say:
CLR via C#
The Common Language Infrastructure Annotated Standard
Essential .NET, Volume I: The Common Language Runtime
Framework Design Guidelines: Conventions, Idioms, and Patterns for Reusable .NET Libraries
are all either specifically about the CLR, or heavily address the CLR and it's design.
JIT internals is an excellent article that covers the innards of the CLR extremely well.
For educational purposes, the SSCLI can be a very comprehensive source for learning about a "typical" implementation of the CLI standard. Though there are some extensive differences between the CLR and SSCLI's implementations (especially in performance related issues), it's still a valuable source for anyone looking to learn some more in-depth details about the CLR.
There's also a useful book that can aid you on your journey into the depths of the source: Shared Source CLI Essentials.