There's the Eclipse Fat Jar plugin. In their own words:
The Fat Jar Eclipse Plug-In is a Deployment-Tool which deploys an
Eclipse java-project into one executable jar.
It adds the Entry "Build Fat-JAR" to the Export-Wizard. In addition to
the eclipse standard jar-exporter referenced classes and jars are
included to the "Fat-Jar", so the resulting jar contains all needed
classes and can be executed directly with "java -jar", no classpath
has to be set, no additional jars have to be deployed.
Jars, External-Jars, User-Libraries, System-Libraries, Classes-Folders
and Project-Exports are considered by the plugin. The Main-Class can
be selected and Manifest-files are merged. The One-JAR option
integrates a specialised Class-Loader written by Simon Tuffs (
http://one-jar.sourceforge.net/ ) which handles jar-files inside a
jar. Individual files and folders can be excluded or added to the jar.
Different settings can be stored and re-executed as "Quick Build" via
the context-menu.