I was just chatting with Steve Smith (from IRAQ) about how to register custom controls in 2.0.
In ASP.Net 1.x you needed to add a page directive to every .aspx page in your application (or .ascx). In ASP.Net 2.0, you can define this at the web.config level.

After you add this section to your web.config, you should have complete intellisense access to it from your .aspx pages. In addition, as you will see in the sample above, you can also declare user controls the same way.
Read: Global Controls via the Web.config