ePubEditor is a Java program designed to create and edit ePub files in their native form. Its UI is written using Java Swing, although the intent is to create a new fork which will use JavaFX for its user interface.
ePubEditor currently supports ePub version 2.x, but work is underway to add support for ePub versions 3.x.
I have two target audiences for ePubEditor: people who have created an e-book in HTML format, and now want a quick and easy way to turn it into an ePub, and people who have ePubs that do not display well on their devices because of "over-styling" and who want to clean up those ePubs for their own purposes.
User documentation for ePubEditor can be found at https://lpassey.github.io/ePubEditor.
For instructions on how to create a new ePub, see https://lpassey.github.io/ePubEditor#new.
For instructions on how to import, edit and clean an existing ePub, see https://lpassey.github.io/ePubEditor#import
As always, project and source code files can be foud here.
Update: Changes to the W3C EPUBCheck library has rendered it virtually unusable by programs such as ePubEditor. Given this fact, references to EPUBCheck from inside ePubEditor have been removed. It is possible to fork and re-implement the programatic interface, but that is a low priority item. For those committed to using EPUBCheck you must compile your ePubs first, then run the EPUBCheck utility from the command line.