Well we all know it is really easy to deploy web parts and other features with WSPBuilder.
When it comes to deploying custom controls, it needs only the DLL to be deployed (and other additional artifacts that you may have with the control).
To deploy the dlls and create SafeControl entry with WSPBuilder:
create the Setup.exe.Config file and add the following two lines:
<add key="IncludeAssemblies" value="true" />
<add key="BuildSafeControls" value="true" />
That's it build the WSP again and deploy your custom control.