It seems that many windows programs that use MD5s have taken the liberty of creating their own file format. MD5 supports the most common formats (there is a pretty well established format for md5's on *nix systems using the md5sum tool). Since MD5 files usually have no header, I'm not sure how I'm going to distinguish between all of them.
However, keep posting links or examples of programs that are not compatible with hkSFV, and I will do what I can to get them all working well together..
(The FreeBSD example posted should be identifiable, since each line has a sort of header [MD5 (...) = ...])