If you're using TortoiseHg you can do this from the Repository Explorer - in fact I do exactly what you're trying to do for a Wordpress install.
thg log
will bring up the log of the repository in TortoiseHg. You can then right-click on a changeset and select (from memory, sorry) Archive
. There are a few options, but you should see an option on the resulting dialog something like "Archive only changed files". Make sure that is checked, and away you go.
The command that's executed is shown to you, but to automate it on the command-line you need to get the list of files changed (see Macke's reply). With a little batch-magic you can feed that into the Archive command.
Have a look at this StackOverflow question for details of how to do it on the command-line, providing you have a SED interpreter installed, which you can easily find for Windows.