The only CIL book on my shelf is Expert .NET 2.0 IL Assembler by Serge Lidin. In terms of what the individual opcodes do or mean, the Microsoft documentation on System.Reflection.Emit has some pretty good information. And it's always useful to look at existing IL with Reflector.
Edit: CIL (and indeed the CLR in general) has not changed at all between .NET 2.0 and .NET 3.5 -- the underlying runtime is basically the same, modulo fixes and performance improvements. So there's nothing newer available on a CIL level than what would be in a book on 2.0
