QR_Encode.h #includes string.h and stdlib.h for no real reason. Also it #defines the ZeroMemory macro, which in my opinion should be defined in the .c file only (if it's necessary at all).
Added target 'clean'. Added dependency on QR_Encode.h.
EncodeData() is the only function mentioned in .h, so all others can actually be declared static, as they are only needed within the .c.
As mentioned in issue #4, binary files should be opened using the mode "wb" to avoid corruption on systems that use CRLF as EOL (mainly Windows).