Custom Controls are controls generated as compiled code (Dlls), those are easier to use and can be added to toolbox. Developers can drag and drop controls to their web forms. Attributes can, at design time. We can easily add custom controls to Multiple Applications (If Shared Dlls). So, If they are private, then we can copy to dll to bin directory of web application and then add reference and can use them.
User Controls are very much similar to ASP include files, and are easy to create. User controls can't be placed in the toolbox and dragged - dropped from it. They have their design and code-behind. The file extension for user controls is ascx.