I'm wondering if there are any implications (unpleasant side effects) for the sysadmin (or any other users, for that matter) that might arise from having files in /usr/bin or /usr/local/bin whose names happen to end with a carriage-return character (even though these are just symlinks -- or I suppose they could be hard links -- to some other file with a normal unix file name).

For instance, if someone just does "ls /usr/bin" in a normal shell window, there's a good chance they will see something that does not reflect the directory's real contents, because at least one line might have an unexpected "\r" in a non-rightmost column of the listing. This could be very confusing, disorienting, possibly even frightening, if the user doesn't know about or consider the possibility that some file names contain "\r".

If your sysadmins and other users are willing to cope with that sort of anomaly, then there's really no problem -- unix file names can encompass any sort of bizarre content (except null bytes), without really causing any serious trouble, provided that users are aware of the situation and of the potential risks of not handling it properly.