We should add a link in the left for Tomcat 6.0 in the JIRA docs. They can pretty much point to the Tomcat 5.5 docs. The only change I can see is this:

4. Update Tomcat Libraries

Tomcat does not come with some libraries required to run JIRA. To fix this, download jira-jars-tomcat5.zip (1.2Mb), and copy the contained jars to Tomcat's common/lib/ directory.

The directory is now just /lib/ rather than common/lib/.