After you download the source archive and extract the source tree, change to the top directory of the windowgrouper-applet tree. You can build and install Windowmake with the following commands:
./configure && make && sudo make install
This will install the applet under the /usr/local prefix. You may need to tell GNOME where to look to find the Windowgrouper applet. You can do this by editing the file /etc/bonobo-activation/bonobo-activation-config.xml and adding /usr/local/lib/bonobo/servers to the searchpath.
Alternatively, you can tell the configure script to install in the /usr prefix (or in which ever prefix your GNOME installation happens to be). This way, no further configuration is required. Here are the commands that I use:
./configure --prefix=/usr --libexecdir=/usr/lib/gnome-panel && make && sudo make install
Alan Briolat has put together an ebuild for Windowgrouper (Thanks, Alan!) which can be found here.