I found no satisfying integration-examples that included upload-support for FCKeditor, so I decided to try to make the integration myself. As far as I've tested, you can upload whatever you want, only limited by settings in FCK and Domino restrictions.
Flash animation of the integration in action. Shows upload of an image and upload of a flash game.
Although it was a bit hard to hack around Domino restrictions regarding uploading files, I finally found out how to make it work.
The interesting bits are the fckconfig.js page, the demo form, and the fckupload form. Read Ferdy's article to understand how you can upload files to Domino without using a Domino generated File Upload Control.
Requirements for the demoapp:
fckeditor in [Notes/Domino-path]\data\domino\html\js\fckeditor