For the main part of the application, I highly recommend Eclipse RCP + EMF (Eclipse RAP is also a plus, since you can use one application for one application and get a free Ajax application for web applications).
If you need to access your own functions, you can always write it in another language or use JNI or implement the IPC form or use web services (SOAP) or REST-JSON or DBus or any other favorite communication mechanism that you like.
I sometimes call Linux tools from my Java application to do the job (for example, “ssh someserver” or “rsync”) and feel comfortable. I don’t find it an urgent reason to get a “pure SSH library for Java” or a “pure Rsync library for Java” when other tools do the job just fine and I can do the next interesting thing.
By the way, I am inclined to Eclipse and JVM (Note: Java is not my favorite, I prefer Scala and Groovy, but it is easier to work with EMF in Java), I have some experience with. NETWORK. Although there is something good in .NET (one of them is C #, superior to the Java language, but it’s just that the second is a Microsoft package that has more functionality than Sun / Oracle, provides Java [SE] API), there are some things you need to consider.
Cross platform first. Although there is Mono, in general .NET is difficult to port. Although you may not need this, it may come in handy. In addition, Eclipse RCP is not only “more cross-platform”, but also surpasses the functionality provided by the .NET Framework. (I know this is not a fair comparison; it's fair to compare it with Visual Studio Shell)
The second is the license, then the instrument and the cost (three elements). All Eclipse tools available. They are open source (you can fix any mistake, make corrections). The license is open, and you can correctly create commercial products on top of it.
The third is functionality. There is so much functionality inside RCP, in combination with EMF, other Eclipse projects, and the rest of the Java ecosystem (not to mention the JVM languages), you have many possibilities for core functions.
See also: http://eclipsedriven.blogspot.com