I suspect ubiquity beats anything else. My inkling is MP3 will kick around for a long time, in terms of widespread support, much like JPEG. AAC's widespread use suggests something similar. But then this is also why I'd recommend first ripping to lossless. WAV is very likely to be around for the very long term, and will include a straight copy of the highest quality from the CD. Whatever formats then show up in future, you can relatively easily convert across your backed-up data (assuming you spin up the HD every now and again, to ensure it's still alive).
As for iTunes, I don't recall it ever 'taking over' anything. I know some PC users get weirdly annoyed at the way it files and organises documents, but that's an option rather than mandatory. (Personally, I've always liked that. The iTunes folder structure is entirely open, unlike the opaque database structure in the likes of Photos.) Metadata is optionally downloaded, too. This stuff's all in the General and Advanced tabs of the app's preferences.
