Are you asking how to make an executable JAR using Eclipse, where the complication is the inclusion of the external libraries?
These guys are great:http://www.eclipse.org/forums/
The folks at the "Newcomers" area, especially Russell Bateman, have been tremendously helpful.
When I do an File->Export, I choose "Jar File" as a destination instead of "Runnable Jar File". The last page: "JAR manifest specification" lets you indicate the application entry point that will run when you click on the JAR file. Thus, you have an executable JAR. The option on "Runnable Jar File" frankly mystifies me. (Not difficult to do.
) One has to select a "launch configuration"?! I have not worked with such objects. And there seems to be no need since simple JAR exports have worked fine for me so far.
One gotcha I run into is that one should double-check the tree on "JAR File Specifications"(second page of export). Expand it completely and make sure all the packages needed are checked, including clicking on the constituent packages to make sure all the class files in them are also checked. (If your cursor is on a given class file when you click export, the default might be to only export that single class file.)
Sounds like you may already know about Properties->JAVA BUILD PATH->Libraries. When I do a WAR export, I have to make sure all the needed libraries are ALSO included in Properties->Deployment Assembly. Seems like needless duplication to me, to have to specify libraries in two places. But the folks at Eclipse have their reasons, I'm sure.
My apologies in advance if this answer is at too basic a level. (A risk when a nOOb attempts to answer a topic.)