The MD5 hash function is dangerously unusable at this point. I
was under the impression, casually following crypto over the last
couple years, that it was weak but likely “good enough” for
non-military, non-banking types of applications. Dead wrong.
There are now known attacks — and doubtless toolchains for specific
exploits — that permit creating two completely different (but valid)
pieces of plaintext that generate the same MD5 sum.
See http://www.doxpara.com for an example of two mocked-up HTML pages,
one for “Lockheed” and one for “Boeing,” that share the same MD5 hash
sum.
See also Wikipedia's MD5 entry (which does not NEARLY sufficiently raise the alarum on this) at http://en.wikipedia.org/wiki/Md5
You might pooh-pooh my admittedly somewhat superficial take on this,
but ignore me at your peril: bad guys are doubtless developing toolkits
for creating two docs, one legit, one malicious, that share the same
MD5 sum.
Bottom line: time to use SHA1 (for a while until someone figures out
how to do the same thing). Simple enough on debian; “sha1sum” is
in coreutils and is a seeming drop-in replacement for MD5 sums.