Well while collisions are cryptographically significant, they don't
necessarily impact any operational security of the the hash. (Since the
collision merely means that there are possibly two inputs which will hash to
the same digest).
As I have no crypto background to evaluate some of the (potentially wild
and erroneous) claims being made in the popular press* (eg
http://news.com.com/2100-1002_3-5313655.html see quote below), one thing
that comes to mind is the safety of ports. If someone can pad an archive
to come up with the same MD5 hash, this would challenge the security of the
FreeBSD ports system no ?
* "MD5's flaws that have been identified in the past few days mean that an
attacker can generate one hash collision in a few hours on a standard PC.
To write a specific back door and cloak it with the same hash collision may
be much more time intensive. "