Grail's comment pretty well covers it, but there is also the control over optional features. Most programs will have optional features that can be toggled in the configuration stage, as well as optional dependencies that may or may not be availabe in the official package.
An example I can think of is sftp support in konqueror in the official Slackware KDE packages (or at least the semi-official ones that Alien BOB created which are generally the same). The official package lacks the support because there is an optional package missing from the base system therefore you would have to use something like fish if you were wanting to do file transfers graphically via the GUI. However installing that missing package and rebuilding part of KDE allowed me to have sftp support.
Also note that some systems make building from source much easier than others. Also note that if you use a system with a package manager, which most distros do have, it's best not to simply install the program with "make install," but rather to compile and create a package that the package manager can install, because it makes for a much cleaner and flexible system as a whole when it comes time to add, remove or upgrade software.
Last edited by damgar; 10-20-2010 at 10:52 PM.