I recently downloaded the jdk 1.3 for linux and I also had the bin..bin file. They said it was a self executable binary, but it turned out that the file was just a tar archive. (let me double check) yes... I just ran tar -xvf j2sdk*.bin and the files spewed out. works great.
I always run tar -tf whaterver.tar before extracting, just to be sure about directory structure.