I just published a stand-alone Java Decompiler GUI (based on Jad) which you can get from Util Java Decompiler (JAD based) v1.0
This is a Windows based .NET 4.0 application, which supports the drag n'drop of *.jar files.
The code that creates that tool is a simple C# script (which you can see here: https://github.com/o2platform/O2.Platform.Scripts/tree/master/3rdParty/JAD ), so it would be easy to extend it to allow for the batch decompilation that you want to do.
It might be good to add support to the other Java decompilers, since JAD sometimes is not able to decompile some files.