These are bdiff patches that the installer applies to .NET's machine code DLLs (e.g. mscoree.dll, mscorwks.dll, mscorjit.dll, etc.) after they're installed on the user's computer.
For the most part, the patches just redirect imports from system DLLs (e.g. KERNEL32.DLL) to our wrappers (e.g. CORKEL32.DLL), except in the case of mscorwks.dll which also requires a patch to disable SSE2 since those instructions do not work on Windows 95 (even if the CPU supports them).