I never thought to change the URI in the plugin, probably because I was using some manually included absolute uris in the theme I was testing, so that is why I used the .htaccess rule.

In most cases though your code should do the trick and it means there is only one thing to change to put it back again.

In addition to filtering out the theme_root, I also had to filter the theme_root_uri using:
add_filter('theme_root_uri', 'theme_root_uri_intercept');
function theme_root_uri_intercept($root) {
return "http://localhost/wordpress-files/wp-content/themes";
}

I’ve found the following on the Microsoft site which seems to be what you were referring to.

http://www.microsoft.com/technet/sysinternals/FileAndDisk/Junction.mspx

You’d do this:
cd /var/www/first/wp-content
rm -r plugins themes
ln -s plugins /var/www/base/wp-content/plugins/
ln -s themes /var/www/base/wp-content/themes/
cd ../../second/wp-content/
rm -r plugins themes
ln -s plugins /var/www/base/wp-content/plugins/
ln -s themes /var/www/base/wp-content/themes/

I didn’t use Windows in a while, but i *know* that NTFS filesystems can handle so-called “symbolic links”, but the feature is not extensively documented, and there is no tool to create them in a default windows setup. However, a compagny named “Sysinternals” had created such a tool and distributed it as a freeware. Meanwhile, SysInternals has been bought by Microsoft, but a few months ago, i know one could still download those tools from microsoft website for free.

Just Google it :D