For example if you use TIBCO Rendezvous, your project uses a tibrvj.jar file which is dependent on a native libary, for example tibrv.dll on Windows. Of course you can solve this by setting a Run Configurations 'VM argument' to -Djava.library.path=
You would think you can do Project -> Properties -> 'default java library path' - or so.
Or maybe Windows -> Preferences -> 'default VM arguments'. But neither exists :-(
That's the part where I say the GUI design of Eclipse could be improved: it's not quite obvious that you can actually edit properties of a jar file in 'Referenced Libraries'. You add jar files and they look like non-editable references to files. But you can actually change some properties.
Select your jar file and do a right-mouse-click:
In this dialog you can specify the path to a dependent native library which is then added to your java.library.path for every existing and future Run Configuration of this project.
Another interesting jar-file setting is the 'Javadoc Location'. Once you specified the path to a Javadoc's index.htm, the online documentation will be available when you program against that API (IntelliSense and F2 work). For TIBCO Rendezvous however, there's no real Javadoc part of the product.
Please note, though, that when you upgrade to another version of the jar file, these jar-file settings are lost. You have to repeat the steps above. It would be nice from Eclipse to be asked whether to keep Javadoc Location/Native Library settings when upgrading a jar file.