In iTunes you can convert them for use with your iPod.
In your iTunes library, select "podcasts" you should have all the podcasts listed, highlight one of them, in the navigation bar at the top of your screen select "Advanced" and then "Create iPod or iPhone version". Once they are converted they will be located in the movies section of your iTunes library. Connect your iPod, when your iPod shows under devices select it, click the movies tab and tell it to sync all movies, apply the settings and sync up, you are good to go.
This is not an Apple issue. I did not create my podcasts in the right format they are Quicktime movies and you need to use iTunes to convert them in the future they will all be in the right format.