Hacker-proof has more to do with installing security patches to your OS (regular info available via linux newsgroups etc ....), prompt control panel updates, and the right server configuration, amongst other things ......
As for a typical *nix based server, the choice of the control panel software (cpanel/whm, plesk, hsphere or no control panel at all) determines which softwares come by default on your system and which dont.
For a good basic configuration, my personal pref is:
1. cpanel/whm
2. Full SSH access (command line based remote access to the server)
3. PHP 4.3.11
4. MySQL 4.1+
5. Apache 1.3.x (not apache 2)
no need of fantastico...... all the scripts that are included with fantastico can be downloaded from the net and installed on-demand. Also, this way you are not tied to the version of a software script that comes with your current version of fantastico. You can install the latest direct from the source site.