<p>Can someone explain when to use each of these?  They almost seem interchangeable in many cases.  </p>

<p>The Custom Control gets added to the toolbar while the User Control (ascx) can not.  The Custom Control does not get rendered in the Designer while the User Control does.  Beyond that, how do you choose which is the right one to use?  </p>

<p>Also, I am looking for the best way to access the controls from JavaScript (GetElementById).  So, a point in the right direction for adding client side support would be great.</p>

This is from Microsoft's site:
Web user controls
Easier to create
Limited support for consumers who use a visual design tool
A separate copy of the control is required in each application
Cannot be added to the Toolbox in Visual Studio
Good for static layout
Web custom controls
Harder to create
Full visual design tool support for
consumers
Only a single copy of the control is
required, in the global assembly
cache
Can be added to the Toolbox in
Visual Studio
Good for dynamic layout
http://msdn.microsoft.com/en-us/library/aa651710(VS.71).aspx