may be good idea to follow all apache configuration files ( for mod_plsql for example ) because those ports can be used to Portal for example. Just see at bottom of httpd.conf 2 references to another conf files.

If one of the upgrade JVM of Oracle will run rmjvm script this will delete ALL java objects ( included all Your developed classes )

Intresting point that on upgrading from one version to another of JVM to ,succseed , you need to add some hidden parameter _system_trig_enabled = false , restart DB
and remove it latter
( sorry i do not remember correct name of parameter try to search on metalink or otn)