Mac OS is pretty much the only thing that knows how to handle resource forks. When you copy to Windows, the resource fork disappears, as well as some useful metadata.
As Mac 68k apps store all their code in the resource fork of a file, everything disappears. PowerPC applications might keep their code, but they would lose all internal resources (including the resources which tell the system how to use the code).
Data copied from Macs absolutely must be archived and compressed by a tool such as BinHex or Stuffit while the files are still on the Mac. Otherwise, a lot of critical data is not moved with the rest of the file.