The advantage of vendor packages
The advantage of using vendor packages is that someone else worries about taking care of program <X>, tracking upstream releases and bugfixes and security issues, making sure that it works, and (with a decent package management system) mostly handling upgrades from version Y to version Z.
This may seem petty, since after all it's easy enough to keep track of something like Apache. The problem is that without vendor packages, it's not just Apache; it's Apache and GNU Emacs and LaTeX and GCC and Perl and Python and so on without end. Tracking things by hand doesn't scale, especially in an environment with other demands on your time, and pretty soon your local software is quietly rotting.
(By 'vendor' I really mean 'anyone who handles package maintenance for me'; as things like blastwave.org and Fedora Extras demonstrate, it need not be the actual OS vendor themselves.)
This is why the Solaris ssh issues bug the heck out of me; Sun is falling down on its end of this, removing the benefit of them handling ssh for me and replacing it with a big hassle. This is one of the areas where doing a half-assed job is worse than not doing the job at all, because it lets people down partway through.