Custom controls are controls that are developed by the developer
or a third party vendor. Custom controls are not provided along with
.NET.

Difference:

User Control (.ascx file - this is a like aspx page) can only used with in the application where it is developed but the Custom Control can used more than one application because it is an assembly.

User Control can't be added into the tool box of visual studio where as custom control can added.

User Controls can be viewed as a sort of generic controls during the design time.
The proper GUI of user controls can be viewed only during the run time.
But Custom Controls can be viewed during the design time.

User controls are created from existing Webserver and html server controls .
But a developer who creates custom controls have to render every thing from the scratch.

Since the dll assembly of a custom control is being used,a custom control developed in C# can be used in a project developed in VB.NET or any other managed code and vice versa.
This is not possible with user controls.They are language spefic