Dê uma olhada no Projeto do Startup Manager . Talvez não resolva completamente o seu problema, mas é uma boa referência para começar:
As the name suggests, Startup Manager (aka st-m) is an open source startup manager for the Windows platform.
Startup Manager can:
- Make programs start on logon (add items)
- Rename existing items
- Delete existing items
- Disable existing items
- Enable existing items
- Create a batch file with programs that start in a certain order
Startup Manager supports:
- Startup folders (all users and current user)
- Registry sections
- All the run and services sections (all and current user)
- Computer sections: winlogon (userinit and shell) and BHO (browser helper objects)
- Win.ini sections (load and run)