Asp.net Custom controls are basically compiled code, i.e., DLLs. This can be very easily added to toolbox, so it can be easily used across multiple projects using drag and drop approach. Custom controls are comparatively hard to create. 

But User Controls (.ascx) are just like pages (.aspx). These controls are comparatively easy to create but tightly coupled with respect to User Interface and code. In order to use across multiple projects, we need to copy and paste to the other project as well.