I agree with Justin here! I use the links functionality on some projects and it's really handy for some small directories - placed in main content and/or sidebar. And: It's also useable for my clients - just simple and self-explanatory. So I would only vote to leave them in (or as core plugin) or turn into a custom post type (in core or as core plugin). All other alternative/option doesn't make sense to me.

Just my 2 cents.
Dave from Germany :)