Code, code and... code
The WebObjects frameworks comes with a lot of APIs, but you can also find a lot of examples and frameworks from the community.
The main framework that most organizations are using alongside WebObjects is Project Wonder. In this open source framework, you will find code to use JavaMail, to fix bugs from WebObjects default frameworks, various EOF/JDBC adaptors, etc.
Another good framework is WireHose. This framework is especially useful if you build “public” Web sites which need a good security and component system. It’s not open source but it’s free to use since version 4.0
You can find a complete list of frameworks in the wiki.