...

1. Both implements servlet 2.5 and JSP 2.1 API's.
2. JNDI has to be configure manually in server.xml for Tomcat whereas in Geronimo,JNDI has access to all the object references managed by geronimo kernel.
3. JMS is configured manually in server.xml for Tomcat whereas in Geronimo same can be achieved by GUI based Administrative Console.
4. JDBC is configured manually in server.xml for Tomcat whereas in Geronimo same can be achieved by GUI based Administrative Console.
5. web.xml is the default deployment descriptor for both the servers
6. Geronimo has container specific deployment descriptor also know as deployment plans whereas Tomcat does not have any container specific deployment descriptor.

In geronimo most of the configuration can be done using the deployment plan geronimo-web.xml, config.xml or config-substitution.properties. Adding resources like JMS queues, connection factory, JDBC datasource etc can be easily achieved using web based Administrative console. This simplifies the configuration management versus the manual configuration done using server.xml and context.xml in Tomcat.

...

With regarda to Apache Geronimo there is no need for setting up environment variables or classpath. This is take care of by geronimo. Creating database table and database pool can be easily achieved by using web based Administrative Console. However you have to include a <dependency> </dependency> tag and <resource-ref> </resource-ref> tag in geronimo-web.xml so that the resources are visible to the deployed application.
All the other suggestions made in Tomcat only application is equally vaild in this scenario as well.

Tomcat and Apache AXIS

...

For Tomcat to work you have to include the following elements in your CLASSPATH environment variable. The jars mentioned below can be automatically downloaded within eclipse if you have set up the development environment in eclipse. This can be easily achieved by adding a wsdl file in your application and using Eclipse WSDL to Java tool to generate all the required artifacts including your java classes.

...

In case you are unwilling to remove jars from your current environment. May be you want to use your version of jars and geronimo ships a very different version of jars. In that case also geronimo provides an easy configuration. You can configure geronimo-web.xml to add <inverse-classloading/> tag. Using this tag the classloading hierarchy will change to Child First.

References

Following resources can be useful while migrating from Tomcat to Geronimo
1) http://geronimo.apache.org/schemas-2.1/docs/geronimo-module-1.2.xsd.html-^{Image Added} Look for inverse-classloading. You may also want to know more on dependencies, hidden-classes, non-overridable-classes. These all elements will be helpful in modifying the geronimo-web.xml.
2) Learn how to configure JMS with apache geronimo - http://cwiki.apache.org/GMOxDOC21/web-application-for-jms-access.html^{Image Added}
3) Learn how to configure JDBC with apache geronimo- http://cwiki.apache.org/GMOxDOC21/web-application-for-jdbc-access.html^{Image Added}
4) For security related configurations you can refer- http://cwiki.apache.org/GMOxDOC21/configuring-security.html^{Image Added}
5) More on configuring various services- JMS, JDBC http://cwiki.apache.org/GMOxDOC21/configuring-services.html^{Image Added}