The Eye-Fi Share, Share Video, Explore Video and Pro cards can now be configured for FTP transfer (including servers using FTP over SSL) through the Eye-Fi Manager, which runs on both PC and Mac platforms. The "Change" link under Settings :: Web Sharing Destinations offers FTP transfer, accessed by clicking "Add another photo service". The instructions show that it is possible to upload both photos and videos via FTP, but don't show whether it is possible to access a server using non-default ports. Either way, the addition is likely to be a very welcome one for Eye-Fi users.
More detailed instructions can be found in the Eye-Fi support center.