SharePoint makes extensive use of User Controls, They are located in the 12 hive in Template\ControlTemplates.
Examples : Welcome.ascx , Toolbar.ascx,…
The deafult web.config includes the content of this folder and its subfolders in the SafeControls section.

So any user control you manually create and place it in the 12 hive in Template\ControlTemplates is automatically considered safe by the safe-mode parser.