Is there a database or repository of the legitimate checksums for Microsoft system files? We think we have a 0day on DNS for Windows 2003 SP2 using IRC for command and control. (Latest McAfee does not see an issue). I want to compare our customer's dns.exe and associated DLLs with the real ones. (I will grab a fresh SP2 and hotfixed system to do this, but wonder how to do this in future without needed to do this.)
Have you tried the System File Checker? It is designed to scan Windows sytem files and replace the "bad" ones. It's pretty easy to run from the command-line:
You need to verify that Windows file protection was on and run the system file checker (SFC) see this KB article for the registry entries to check and SFC/WFP options. Newer versions of windows verify that the exe/DLL for OS files is signed by microsoft before loading.