This is how I built and configured the CLI (Command Line Interface) version of HandBrake on my 64-Bit Ubuntu 8.04 computer.

Prerequsites

$ sudo apt-get install make gcc g++ jam autoconf automake \
libtool libz-dev devscripts subversion \
libgtk2.0-dev libglib2.0-dev  libhal-storage1 \
libhal-storage-dev libhal-dev

You will also need to build yasm because the version in the repositories is too old.

$ mkdir -p ~/projects
$ svn co https://www.tortall.net/svn/yasm/trunk/yasm ~/projects/yasm
$ cd !$
$ ./autogen.sh  # this creates cofigure
$ ./configure
$ make
$ sudo make install

Checkout and build HandBrake

$ svn co svn://handbrake.m0k.org/HandBrake/trunk ~/projects/HandBrake
$ cd !$
$ ./configure
$ make

At this point I just created a symbolic link someplace in my path that pointed to ~/projects/HandBrake/HandBrakeCLI

Upgrading HandBrake

If at any time you need to upgrade to a newer build of HandBrake, just do the following.

$ cd ~/projects/HandBrake
$ svn up
$ ./configure
$ make clean
$ make