Flash .swf and Unity .unity3d files can now be uploaded as games! These can then be embedded in the game page itself, but you'll have to handle the embed tag on your own for now. Just use the absolute URL for the file that the submission page spits back at you once you upload the file.
Additional files for the game can be attached at the bottom of the form as well. Check the Klik of the Month #36 invite for an example!