At Stack Exchange we use Bosun to monitor both system and application metrics. As an application developer I get pretty much everything I need on the system side out of the box with scollector. We spend a fair amount of time on projects now developing application-level metrics, which we use BosunReporter [0] to send to the same instance. It's quite useful to have application and system metrics on the same tool.
[0]: github.com/bretcope/BosunReporter.NET