If you're deploying a custom plugin:
You can edit /opt/atlassian/jira/atlassian-jira/WEB-INF/classes/system-top-navigation-plugin.xml and change many things there – but I don't believe you can change where the logo links to.
What I've done is add another option to JIRA home by adding the following into my atlassian-plugin.xml to contain the following:
<web-item key="set_my_jira_home_custom_plugin" name="Set My JIRA Home to CUSTOM" section="system.user.options/set_my_jira_home" weight="10"> <label>My Custom Plugin</label> <link linkId="set_my_jira_home_custom_plugin">/plugins/servlet/my_custom_homepage/</link> </web-item>
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