The macintosh OS (not sure about OSx) uses a dual forked file system, unlike the rest of the world ;-). Every macintosh file has a data fork and a resource fork. When a dual forked file hits a single forked file system, something has to go, and it is the resource fork. This was recognized as a problem (bad idea to begin with) and apple started recomending that developers avoid sticking vital file info in the resource fork portion of a file, but some files are still very sensitive to this. The main ones to watch out for are macintosh font files and executables, once the resource fork is gone from a mac font or an executable it is useless. To protect the files they should be stuffed or zipped prior to upload to protect the resource fork.
Most mac ftp clients (like fetch) allow files to be uploaded in Macbinhex, which will also protect the resource fork when transfering files via ftp. I have not seen this equivilent in any mac browser (but I haven't done too much digging either).
FYI, apple does have an old utility called ResEdit that lets you manipulate the resource fork portion of a file.