If you want your Domino Server to start as a service then you can do as follow:
1. Open Start -> Run: regedit
2. Go to HKEY_LOCAL_MACHINE -> System -> CurrentControlSet -> Services -> Lotus Domino Server -> ImagePath
3. Double click on ImagePath and append -jc params to the end.
"C:\Program Files\IBM\Lotus\Domino\nservice.exe" "=C:\Program Files\IBM\Lotus\Domino\notes.ini" -jc
4. Quit Domino Server and start it again, it will ask you to run as a service.