You app pool will be spun down after 20 minutes of inactivity, this is standard IIS behaviour.
To avoid this, you can upgrade from Canoe to either the Catamaran or Yacht plans. Web apps on those plan don't idle (adding a custom hostname, SSL or running more than one dyno on the Canoe plan will still give you an idling app).
You can also circumvent the idling by using services like Pingdom and StillAlive to generate requests for your site. But upgrading from Canoe is fairer to AppHarbor.