Well .NET assemblies are the easiest to change. Easy way is to get Telerik's JustDecompile and add the Reflexil plugin. Modify the instructions and recompile. Note that you may have to run it through a deobfuscator and depending on what was used, naming conventions may make this a bit difficult.
I can't suggest anything for non-MSIL executables purley because I don't know. Does this help at all?