Wrong. You can use the NetBeans Platform to create a server side application! Your components just stay the same (of course, if you properly separated the models and controllers from the GUIs) and you can just reuse the binaries (OSGi people are probably acquainted with that, especially since when Glassfish supports it - the news is that the NetBeans Platform can be used as well).
Indeed, Jaroslav Tulach already talked two years ago about the NetBeans Platform on the server side (hell, is there in the world something that that guy hasn't done yet?), with a project name "DVB Central". As Tim Boudreau wrote, DVB central is a "bare bone" Platform (basically the BootStrap, Startup, File System, Utilities, and Module System APIs) deprived of any Swing part, that contains a small HTTP server used for remote administration.
My needs (because - you guessed it - I'm talking of a real-world scenario here) are more complex: I need to reuse more NetBeans Platform modules (e.g. DataObjects); the application should not be a "standalone application embedding an HTTP server" but a regular web application deployable as a .war within Tomcat; and I also need to use a web framework for it (namely, Wicket). Furthermore, the application needs to expose a WebDAV interface and some REST modules.
While it took a while to get to it, the currently polished solution is cleaner than I expected, and I'm going to show you how it works. The project that is build on it is blueOcean, a new member of the blueMarine family. It is basically a "server side" blueMarine, with the non GUI modules that implements the cataloguing system. While it's not yet entirely available as a complete application (it's rather a base platform that I'm using to create the customer's application, which has the user interface), it is available since one or two days at blueocean.dev.java.net and you can look at it for seeing the technical solutions I'm going to illustrate (and in a matter of weeks the website blueocean.tidalwave.it should be born). Please be aware that this article assumes that you have some basic knowledge about deploying .war applications and also about how NetBeans Platform applications are made.