I want to know whether it will affect users if I reboot my server? Can I find out who is currently logged on to my Windows Server 2003?
If it is a DC the effect will be that users cannot authenticate to that DC until it's back up (that may or may not be an issue depending on your environment)
For remotely checking who is currently logged in PsLoggedOn is a great tool.
Example: Psloggedon \\ComputerName/IPaddress