To which package does your /etc/mime.types belong? -- 'pacman -Qo /etc/mime.types'
If that doesn't help, run 'find /var/lib/pacman/local/ -name install | xargs grep -l mime.types' and have a closer look at the results.

Eh, okay, there's a mime-types package now. I'll read more closely next time... ;-)
Nevertheless, the file looks fine here, so maybe the find run from above might still prove useful.

Yes, you are right. My reasoning was hollow. (And I wasn't aware of how pacman treats the config file versions.)
There is a normal "mime.types" file in "mime-types" package. But grepping (that you suggested) discovered, that the file "/etc/mime.types" gets corrupted during the installation of "jre" since "/var/lib/pacman/local/jre-6u2-1/install" has the following:
if [ -f /etc/mime.types ] ; then
mime=$(grep -v 'application/x-java-jnlp-file' /etc/mime.types)
echo $mime>/etc/mime.types
fi
echo 'application/x-java-jnlp-file jnlp' >>/etc/mime.types

I am not an experienced linux user and I don't know whether:
$ a=`echo -e "1\n2"`; echo $a
1 2
is the right behavior.

However, I'd suggest to replace that chunk of code with:
grep -qs 'application/x-java-jnlp-file' /etc/mime.types || echo 'application/x-java-jnlp-file jnlp' >> /etc/mime.types
and also something sensible for post_remove,
BUT is the "/etc/mime.types" file expected to be modified by package installers?

I think that this is a duplicate of the highly annoying 6801 and that the comment by Antox includes a possible solution.