Ubuntu has recently released an upgrade for tomcat 6. If you have installed webapps that need a particular configuration of heap or permjam or any parameter that you want to pass to catalina engine... well you'll have to rewrite your config since catalina.sh and your setenv.sh in /usr/share/tomcat6/bin are going to be overwritten.
If you have, for example, installed liferay and upgraded it to version 6.0.6 you are likely to have problems my frieds; it took me a whole day to understand what was going ( literally ) tits-up in my server since i noticed an exception in liferay that I thought I already had fixed with the use of portal-legacy-5.2.properties.
Said that I would like to thank the guys at Debian and at Ubuntu for their great job ... and I can't help but ask them to pay a little more attention when they release upgrades that impact server releases of their stuff.
hope this helps someone out there