Maven was designed, in fact,
precisely to save you this kind of pain.
You can use the special Maven goal "eclipse:eclipse" to have Maven construct the necessary files to make a Maven project eclipse-friendly. There's also an IntelliJ goal for that
IDE.
I have some very complex projects. They're built on Spring, Hibernate,
JBoss RichFaces, and often include additional subsystems like javamail and Quartz Scheduler. It can occasionally be frustrating, because once you get that much stuff in one app, they can start fighting over conflicts on shared resource versions. But one of the strengths of Maven is that once you find a "magic combination", Maven will lock the project to the specified versions and not break as soon as one of the contributing components gets updated.
Of course,
finding the magic combinations is the real challenge. Usually I end up reading other people's blogs. Shared suffering.
One thing that can really help you get started is archetypes. There are quite a few published archetypes for different types of Maven projects. Plus, it's actually pretty easy to define your own. Although a lot of my webapps have been simply cloned from earlier maven projects, occasionally, I'll use an archetype to start a project from scratch.