<p>Nowadays, we have tons of Javascript libraries per page in addition to the Javascript files  we write ourselves.  How do you manage them all?  How do you minify them in an organized way?  </p>

First of all,
YUI Compressor
.
Keeping them organized is up to you, but most groups that I've seen have just
come up with a convention
that makes sense for their application.
It's generally optimal to
package up your files
in such a way that you have a small handful of packages which can be included on any given page for optimal caching.
You also might consider dividing your javascript up into segments that are
easy to share
across the team.