Depends on how you installed them, but a Jira install is usually quite clean - it will have put it all in two directories - one application directory (e.g. /opt/jira) and whereever you set the "jira home" to (e.g. /data/jira). Delete those two, and Jira is gone. Of course, if you've written supporting scripts, split the data up (I put attachments outside "jira home" for example, as I usually need it on a separate file system for backups/replication), and so on, you coul dhave files in other places.
MySQL, I'm not so sure - I've only ever installed in on a Linux box, and never removed it using anything other than apt or rpm to remove it, which I've just assumed will clean up for me.
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