Some of these are "better" than others, but I've yet to see one that completly eliminates the risks, though they reduce the window for failure to the point of reasonable risk.
I would (perhaps naively) think that renaming the original file (renaming should be atomic, no?) to something like "$filename.$$", then reading / munging / writing to "$filename", and only deleting "$filename.$$" when the new filehandle is closed (and thus their buffers flushed as well as Perl can make them) would completely eliminate the risk. The process could stop at any point and, at worst, you'd have a partially munged new file and the original file both existant. Assuming, of course, that you have a sufficiently paranoid filesystem.
I'm not entirely sure I'm not missing something, so please enlighten me if I am. =)
Black flowers blossom
Fearless on my breath