Windows reboot to safemode from command prompt
Solution 1:
In Windows Vista and later, the command
bcdedit /set safeboot Minimal
will enable safe mode (of course you must run this from an administrative command prompt) and the command
bcdedit /deletevalue safeboot
will turn it off again.
Solution 2:
I'm not aware of a built-in command line method. You could in theory write one that sets the boot.ini flag and reboots the machine, though.