for jira you could at least enable Dark Features to get this header and add custom navigation to it
the full functions in the header like app-switching will be brought with jira 6.
to activate it in jira 5 do this:
open your $jira_host/secure/admin/AdvancedApplicationProperties.jspa
add "com.atlassian.jira.darkfeature.CommonHeader" to the value
refresh -> Done
if you want to add custom applications to the navigator (top left corner) do this:
open your $jira_host/plugins/servlet/customize-application-navigator
add Name & Url
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