The only issue I ran into, when migrating from Tomcat 4x to Tomcat 5x, was the value printed when using <
jsp:getProperty .../> tags. In 4x, if a property was null, the tag would print an empty
string. In 5x it prints the literal 'null'. I've seen some other people, who were trying to use non-bean objects with the useBean tag, complain about the JSPs not compiling.
For the most part, if you've written your app to the specs, the migration should be painless.