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That really depends on what you want to do.
You could probably monitor tomcat with a web scenario or just with procs running.
I e.g. monitor mysql with a little shell script/conf file I include in zabbix_agentd.conf in the user defined parameters section. In the conf file I define keys and the call to the script that generates the data.
Alternatively for mysql there is a solution from fromdual http://www.fromdual.com/mysql-performance-monitor which looks quite good.
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