Hey,
It's a way to specify assemblies that are "default assemblies" so you don't have to reference them. That is it's purpose; you can still use using/import statements in your code-behind and it will work fine. I would leave existing ones there as other components may rely on that.
Hello Krzysiek welcome to SO :-).
To answer your question you are probably referring to the web.config file's assembly section for your asp.net web project. The assembly section simply defines a reference / dll file that your web site may use. For instance, assume you had to write a web application that displayed a flowchart representing your workplace hierarchy.
In this case you noticed that it would be quite difficult to do such a thing from scratch. Your next best bet is to find someone who has already implemented say hierarchies in asp.net. You may find a free one but most would charge you some sort of fee. Once you get this piece of software you need to define it or reference it. That is where the assembly section allows you to define as an example a compiled dll.
Your web.config assembly section will then list it with any other relevant information. Unless you know what you are doing it may not be so wise to simply delete an existing defined assembly.