The biggest problem, in my mind, isn't backing up the messages themselves. You can configure a POP downloader and leave it at that.
The biggest problem is backing up the metadata. I don't have a complicated labelling/tagging system --I depend on search a great deal--, but I need a limited segmentation otherwise the mass is completely out of control. I organize by Life Sphere (Personal, Academics, Business), and by Project, anything beyond that is masturbation given return on time invested (for me). Clearly I can get the messages out of GMail trivially, but how do I get the metadata out? That's the serious problem in my mind.
IMAP folders don't work. They're exclusive labels, which don't work for me. I need to be able to express the reality that something may be both Business & Personal (however unfortunate a reality that may be) or that something may be Project: 123 ABCDE St., and both Mechanical and Acoustical (saying that it's one, when it's actually both is silly), because it's plumbing that needs to sound-proofed.
Ideally, we need IMAP with hierarchical, but non-exclusive, arbitrary metadata. I.e. your friend Amy who you're collaborating with on a project can be found under People->Friends->Amy or People->Business->MyCoolProject->Amy. And it has to be a standard. And everyone has to respect it.
Photographers have XMP, IPTC & EXIF, but now everything goes inside XMP. This is good and makes sense. I want the same for my email (and my bookmarks, my notes, my documents, my music, my video...). Metadata represents our investment in time, organizing our ridiculously over-complicated lives. This shit is serious. Archiving data without archiving the metadata is going to become more and more useless as these piles of data grow bigger and bigger. Without metadata finding a photo I took two years ago that I loved would be completely friggin' impossible. It's already happening, and I'm shocked no one is doing a thing about it.
Vendor lock-in is just taking on a different form. Google uses open data formats, and closes the metadata format. We can keep our data, but in a flat POP download we damn well won't be able to ever find what we need...