I am looking for software (like Nagios) that also can monitor my applications. Is there a software solution that monitors both the servers and the applications on those servers?
Dynatrace is APM and infrastructure monitoring solution. It supports a wide range of technologies (including java related stack). It works both as a SaaS and on-premise
Sadly it is not free, but from my experience is worth the price for big deployments.
After much discussion, the consensus is that such a product does not exist and that it may actually be preferable to develop the product oneself.