I haven't delved into Tomcat 6, but if it's anything like the changes from Tomcat 4 to Tomcat 5 you aren't going to be able to just copy and massage the server.xml -- the changes are too vast.
Rather, you may want to start with the generic server.xml (copy it first so that you don't lose it), and add things to it one at a time, testing along the way, until you get all your settings migrated.
I found that it's usually a great opportunity to make sure no "cruft" has accumulated in the server.xml.
Again, this is extraplolating from my experiences with migrating Tomcat 4 to 5; not any concrete experience with 5 to 6. [ January 02, 2007: Message edited by: Bear Bibeault ]