There was a time when the providers of dedicated hosting used to charge their customers for specific software packages. These packages were provided as addition to the hosting services. Mostly, the providers charged a monthly price for them.
With the passage of time the providers started realizing the utility of bundling the software package with the dedicated servers. Thus to day you will find no monthly fees for the software. The main model comes with the software included in them.
For instance when you are using the windows web hosting you may use the SPLA provided by Microsoft. Most of the Microsoft server based products use SPLA or Service Provider License Agreement.
Good dedicated server provider will allow you the option to select the software you wish to have installed on it. Such software might include the operating systems, databases, or any such specific application you desire to have. The servers could be customized to the requirements of the customer.
Sometimes you might use the specialized web hosting programs like the control panels. It includes the software, server, and automation tool applications. All of them could be installed on a dedicated server. The software enables web server integration, applications like databases, programming language and other tools used for server administration. Web based front end in the software enable you to automate the tasks to be accomplished.
It does not mean that use of dedicated server is without limitations. Many providers may not allow you the IRC like bots, clients, and daemons. The reason is that they are apprehensive of dishonest users triggering DDoS attack against the server bringing down the quality of services provided. Many also disallow adult contents or items that are legally questionable.