Custom controls are basically compiled code i.e. DLLs. These can be easily added to toolbox, so it can be easily used across multiple projects using drag and drop approach. These controls are comparatively hard to create.
But User Controls (.ascx) are just like pages (.aspx). These are comparatively easy to create but tightly couple 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.