Custom Controls are compiled code (Dlls), easier to use, difficult to create, and can be placed in toolbox. Drag and Drop controls.
Attributes can be set visually at design time. Can be used by Multiple Applications (If Shared Dlls), Even if Private can copy to bin directory of web application add reference and use. Normally designed to provide common functionality independent of consuming Application.
User Controls are similar to those of ASP include files, easy to create, can not be placed in the toolbox and dragged - dropped from it. A User Control is shared among the single application files.