File formats
As a matter of principle, the files you upload at Savannah need to be created / editable using free software, and the free replacements need to be at least as good as the proprietary one.
Flash/Gnash
In the case of Gnash, it's currently not fast enough. Until the Cairo backend is done, it essentially requires a 3D card, which nowadays almost always run with proprietary software only; this is a non-trivial issue.
If your particular Flash file plays as well with Gnash than with Macromedia/Adobe Flash, there's no problem with uploading it at Savannah. In the opposite case, you're essentially enticing users to use Adobe Flash for a decent "user experience," so that's not a good value to promote.
(2022) Since Flash has been superseded to a great extent by other formats, the above note is unlikely to matter now. But the principle remains.