As BalusC said, this is not JEE related but IDE related. This allows to add "characteristics" to a project in a flexible way.
From the IntelliJ IDEA Q&A for Eclipse Users (because you mentioned IDEA):
Q: Facets — what they are for?
A: To streamline the project configuration.
Facets encapsulate the support for a
variety of frameworks, technologies
and languages. For example, to enable
Spring in your project, you only have
to add the corresponding facet. All
libraries are downloaded and
configured, you get the full range of
coding assistance, refactorings, etc.
Moreover, the code model is also
recognized, so you are completely free
from worrying about any configuration
issues.
In most cases, you can add more than
one facet of the same type to your
project. For example, you can have
multiple Web facets for deploying the
application to different servers, or
several EJB facets, each for its own
EJB version. (See also Project
Configuration.)
And yes, Eclipse uses "Facets" too:

AFAIK, NetBeans doesn't (see Q: How do I configure a web framework for my project?).