I'm using Beyond Compare 4 (4.1.9) in order to compare war files.
I need to compare the files .class that I find in the several packages.
Double clicking on a war file in Beyond Compare's folder compare will expand it as a folder because war files are essentially zip files.
To decompile Java class files to source code in Beyond Compare, install the Java Class to Source file format. With the file format installed, when you double click on a .class file inside a .war archive, it will display the decompiled source code in Beyond Compare's Text Compare.
Download page for file formats: http://www.scootersoftware.com/download.php?zz=kb_moreformatsv4
Note the Java class to source file format is only available for Windows, it isn't available for the Linux or Mac versions of Beyond Compare.