I use to set an alarm to wake me up, but the voice will wake my wife up too, so I want to know that if I can just set the n900 vibrating or just turn on the notification light?

thanks in advance

Renamed the attached file to silent.mp3 then set it as your alarm sound.

There are sh commands on the wiki for vibration and for notification.
And maybe you can listen on dbus events to run them if alarm sends any. If it does you can try using headphoned as an example to start from.