What’s the best way to pair Nagios monitoring with EC2

It is possible to use the ec2 tools in a script to dynamically generate a nagios config. If all EC2 instances need the same services, then you associate the service with a hostgroup rather than a host, and dynamically generate the host/hostgroup definitions with the script run via cron. You can then do a kill -HUP (or /etc/init.d/nagios reload or svcadm nagios refresh) and have nagios reload the new config. This is a lightweight operation (doesn't require a restart) and so can be done pretty often. The script would have to read a list of active instances and their addresses, and generate a host definition for each one.

I use Nagios / NRPE for our JIRA server (which also runs Confluence), together with Munin for tracking resources over time (handy for looking for memory / CPU spikes, excessive DB accesses, etc.)

Apart from the standard checks that come with NRPE, I added the following for JIRA:

• A check_http check that makes sure the application is up
• A check_file_age check that verifies the JIRA backup file has created and is the expected size.

We set up an external SMTP server in our JIRA instance, so there's not much to check regarding email; if you have your outgoing mail server running on the JIRA machine, you could add a Nagios check to make sure its outgoing mail queue isn't getting too full (Munin also monitors this by default). You could also maybe use a WebInject test to log into JIRA and go to the admin page that shows the size of the mail queue.