Currently, the only foreseeable way to check if the user has a particular peice of software installed is to run a command from the software, eg "mysql --help", and then if that returns false, mark that it isn't installed, and add it to the downloads package... that or type -P "command", that way the path will get returned.
Anyways, there are some packages which i would reccomend for security and other purposes would be;
* IPTables - Pretty easy to parse and add to the web frontend, plus a good deterrent for people who are trying to mess with your server.
* Snort/Tripwire - For making absolutely clear how many users are doing what they shouldn't be.
Thats all i can think of atm.