I had the same problem. Ubuntu 12.10 now ships gpodder 3 which uses a new and incompatible database format. They don't appear to have supplied any conversion tool nor any warning that your old config wouldn't be converted (thanks!). However - it seems gpodder3 keeps it's configuration in a gPodder directory in your home dir, while gpodder 2 was keeping it's configuration in .congfig/gpodder. So I was able to recovery my subscriptions.
Here's what I did: from the gpodder download site I downloaded the last release of version 2 (I used this one). Unpack the files somewhere (we don't need to actually install it, just run it once. I put them in /tmp). Make sure gpodder 3 isn't running.
Then from a terminal I ran
Now you can export your subscriptions to an OPML file that gpodder 3 can import (it's on the subscriptions menu). Once you've done it you can quit and run gpodder3. Skip past the initial dialog offering you default subscrptions and you can import the OPML file you created in the last step.
I had an extra problem, because even after this gpodder3 didn't recognize any of my previously downloaded podcasts (it wanted to pull down 3Gb of new shows!). This might be unique to me because I was using a non-standard location for my downloads, but I solved this by the brute-force technique of doing one last sync to my player from gpodder 2 and then telling gpodder3 to consider all the subscriptions up to date. I'm sure we could do better but this was enough for me.