First I decide what I want the server to do. FTP, HTTP, File-serving, Web-proxying. Once I decide on what it is to do, I then move on to how I will administer it, ssh, rdesktop, etc. That tells me additional software I will need to install. Third I write a firewall script to cover the decisions made above. Then it is a custom install of my distro of choice, and installing the software. I always do the server software installations from source, that way a simple recompile can be done without having to wait for a download to add modules or functionality. Hope that helps..
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