I run nagios to monitor certain processes that are running on servers. At the end of the month I produce an uptime report. In my uptime I include all uptime and any periods of scheduled downtime/maintenance. I.e. my uptime percent is everything except unscheduled downtime.
In nagios before taking a service down I schedule downtime for the processes via the web interface. When I go to availability reports and select the service the scheduled downtime is included in the