Look into Puppet or CFEngine (we use CFEngine but am considering switching to Puppet eventually). They're both extremely flexible management tools that will trivially handle package management, but you can use them to accomplish almost any management task you can imagine, with the ability to manage or edit any file you want, running shell scripts, etc.
The work flow goes something like this:
1. Identify packages that need update (have a cron job run on every box to email you packages that need updating, or just security updates, however you want to do it)
2. Update the desired versions in your local checkout of your cfengine/puppet files (the syntax isn't easily described here, but its very simple to learn).
3. Commit/push (note that this is the easy way to have multiple administrators) your changes. Optionally have a post commit hook to update a "master files" location, or just do the version control directly in that location.
4. Every box has an (hourly? Whatever you like) cron job to update against your master files location. At this time (with splay so you don't hammer your network) each cfengine/puppet client connects to the master server, updates any packages, configs, etc, runs any scripts you associated with those updates, then emails (or for extra credit build your own webapp) you the results.