schepp22, have you subscribed to the WFMU feeds through the iTunes listing of podcasts? I have no difficulty doing things this way. iTunes will periodically stop updating some podcasts, but this is always indicated by a ! next to it, and is caused by it not thinking you are listening to them. Podcast-related settings are found on a button on the bottom of the podcasts view in iTunes, also, not in the normal preferences box. And you will find that the most recent shows remain in mp3 format in the archives for some weeks, so if you know how to download archives you can do that. In any case, just delete your subscriptions and re-add them. Unfortunately, WFMU podcasts don't stay put in the podcast feeds; you can usually only d/l the most recent one. This is in contrast to podcasts like Jessup Thune's where if you can "Show all available episodes" and "Get" particular ones.
fred/ricks, in iTunes -> Preferences -> Advanced, do you have "Keep iTunes Media folder organized" and "Copy files to iTunes Media folder when adding to library" checked? It is better to have iTunes manage files and then sort them using the metadata that is internal to the various files. Any files you have added to iTunes, delete from their original location. If you do not do this, iTunes retains only a pointer to your original files and doesn't file them away. On modern file systems it is possible to refer to a particular file in a permanent way not depending just on its name and location, so sometimes iTunes will be able to keep track of files you have added and then messed with, but there's a limit to this. (And don't add playlist files such as .pls or .m3u to iTunes in addition to tracks the playlist refers to; that causes duplication.) Finally, if you have a Mac google for "Doug's Applescripts" for a number of handy ways to munge and correct file information.
There is no limit to how much iTunes can store, but it does get bogged down after a while. I have about 600 gigs of music and about 300 gigs of audiobooks and other content, and I have been continually using the same iTunes library since 2003, all without any serious problems.
Unrelated, but you should make sure you have a complete backup of everything always.