Yes. It works with all types of files. EXE's (obfuscated or not), DLLs, pngs, word documents, etc. Really, anything.
wyBuild compresses best when the different versions of the files are similar. This is always the case for non-obfuscated code. And is very often the case for obfuscated code.
If you have any other questions I'd be glad to answer them.