We are using quite a few Atlassian applications, Bamboo, Confluence, JIRA and Fisheye with Crucible.
In all of these applications, it is possible to overwrite the application name, only in Fisheye/Crucible this is not possible.

1. it will always display "Atlassian Fisheye & Crucible" as title
2. application navigator always will display "Fisheye/Crucible" as name for the application link