I don't have a cookbook solution to that problem, I'm afraid. Upgrading from Java 1.4 to Java 6 is "supposed" to be transparent, because Java maintains strict backwards compatibility. But it's an imperfect world, so occasionally, a "gotcha" will pop up that requires a code mod. In some cases, you may need to run the compiler using the "-source" option to allow for things like earlier versions of Java allowing the now-reserved word "enum" to be used as a variable name. I've run into an app or 2 that did that.
The most obvious differences between Tomcat5 and Tomcat6 are that the 3 lib directories have been replaced with a single lib directory in Tomcat6 and that Tomcat6 provides a built-in EL implementation jar, so any webapps that had included their own EL implementation jar in WEB-INF/lib must remove it.
Overall, however, you shouldn't find upgrading to be too difficult, however.