It is good practise to stick with the distro provided packages because this greatly enhances system maintenance and updates/upgrades.
However, there are cases when the version doesn't cut it. An important service might require it, or a specific local policy demands a certain patch.
If you're going to create custom software, chances are that you need to install it on multiple systems. That's why it is a good idea to distribute and manage them using the same tool as the distro: apt-get. We keep a repository of our custom Ubuntu software packages at http://ubuntu.terena.net.
When creating your own versions, you are responsible for updating the packages and the repository.
Since this can happen very infrequently, I detailed the steps the steps to (re)create the packages and the repository below.