After testing AXIS , I quickly moved on to check the latest Cocoon 2.1.8 release. I'd tried getting earlier versions running with OC4J but given up due to the xerces, xalan and jdk certification mix - it was hell. Fortunately Cocoon 2.1.8 worked (almost) perfectly first time with Oracle Application Server Containers for J2EE 10g (10.1.2.0).
After building Cocoon, I simply used a manual installation with the standalone version, which simply required $ORACLE_HOME/j2ee/home/config/application.xml and $ORACLE_HOME/j2ee/home/config/http-web-site.xml to include the Cocoon webapp.
The only "fixup" required - and this is for a non-fatal SAX processing error - is to force Cocoon to use the XML parsers etc that are included in the Cocoon distribution instead of the default (Oracle) parsers included in the OC4J distribution. The fix is to force "search-local-classes-first. To do this edit $ORACLE_HOME/j2ee/home/application-deployments/<your Cocoon deployment path>/orion-web.xml. Uncomment the line:
<web-app-class-loader search-local-classes-first="true" include-war-manifest-class-path="true" />