I'm surprised that you've got this problem when FTPing programs; my experience has been that ftp usually starts up in ASCII mode (and I usually forget to put it into binary mode, resulting in me downloading a corrupted binary, smacking my head against the monitor, turning binary mode on, and repeating the download). I have seen it when Windows and *ix boxen are networked together; apparently some networking systems are bright enough to manage big-endian - little-endian conversions but not quite intelligent enough to do end-of-line correction.

Ovid's solution is clever. Hacking ftpd may be a "superior" solution, but Ovid would be doing this on somebody else's nickel, and those somebodies may not want to pay for it.