The first major decision to make after you have purchased server hardware is what operating system to use. Many servers come with one already, but if yours does not, you will need to decide on one. Linux or other Unix variants, such as BSD or Solaris are by far the most popular, but there are also many Windows servers out there. If you are on a limited budget, go with a free Linux distribution, such as CentOS.
The next thing to choose is the web server. Choices include Apache, Nginx, and Lighttpd. After that, you will probably one a database server such as MySQL or PostgreSQL Finally, you will want a web-based control panel. Depending on the one you choose, it might also install its own versions of Apache, PHP, and MySQL.
There are many control panel solutions on the market, and most of them are commercial. Popular control panels includ cPanel and Plesk. There are also free solutions available like Virtualmin. Decide what you need for whatever type of websites you plan to have and then choose the software that meets those needs.