If I were you I would declare it directly in the top of your layout.master file so you don't have to maintain that change in Web.config during upgrades.
<%@ Register TagPrefix="user" TagName="Widget" Src="~/Controls/User/Widget.ascx" %>
namespace and assembly are used for declaring server controls, user controls are declared as above when in the page or like this in Web.config:
<add tagPrefix="portal" tagName="SkinList" src="~/Controls/SkinSetting.ascx"/>
Hope that helps,