Some others not mentioned here -
Mono Cecil: With Cecil, you can load existing managed assemblies, browse all the contained types, modify them on the fly and save back to the disk the modified assembly.
Kaliro: This is a tool for exploring the content of applications built using the Microsoft.Net framework.
Dotnet IL Editor (DILE): Dotnet IL Editor (DILE) allows disassembling and debugging .NET 1.0/1.1/2.0/3.0/3.5 applications without source code or .pdb files. It can debug even itself or the assemblies of the .NET Framework on IL level.
Common Compiler Infrastructure: Microsoft Research Common Compiler Infrastructure (CCI) is a set of libraries and an application programming interface (API) that supports some of the functionality that is common to compilers and related programming tools. CCI is used primarily by applications that create, modify or analyze .NET portable executable (PE) and debug (PDB) files.