We are in the process of changing all the show downloads to torrent downloads to speed up the process for everyone. I just added all the torrents for the shows that we lost in the hacking; September 27th, 2006 till today. I've made torrents for every episode you can download which you can download in a couple different ways. You can download a torrent that will download every single show at once, or you can navigate to Radio Shows and download the torrents there. I have updated all the download links back to September 27th, but the ones older than that don't work. Mecha is going to be updating those in the near future. Until then, you can find a torrent list here. Just find the name(file->find) of the torrent you want and click it.
Another note about the torrents, thanks to all you who have seeded. There's at least 4 people that have seeded several shows since I've put them up. I really appreciate it. To all those that are just downloading know that the more you help in uploads the faster your download will go.
EDIT: The entire first page, about every show of 2006, is now ready for your downloading pleasure.