I have spent a considerable amount of time "beating my head against the monitor" trying to get my app to run in Tomcat 4.0.6. It appears that there is some major classloading issue when it comes to loading classes that a) depend on native libraries (e.g. JDBC Type 2 drivers) and b) WebService packages like Apache Axis.
I have tried all sorts of variations of where to deploy the jar files (WEB-INF/lib vs. $CATALINA_HOME/lib, etc.) and nothing works. It is one Exception related to Inialization, ClassNotFound, or UnsatisfiedLinkError (what a mess). I am so frustrated right now that I didn't just use Tomcat 4.1 to begin with that I could faint.
IDEA has to get off 4.0.x because it is not a) not supported and b) I now believe a piece of crap (probably why jakarta discontinued it).
I am curious to hear back from other developers who are using Axis as a client from a Webapp and those that are using Type 2 JDBC drivers from a Webapp and hear your experiences.