I want a DNS replacement that allows you to "subscribe" to TLDs, each with their own policies and practices. Domains are identified by a tuple of a public key and the domain name, so that if someone wants to share a domain, the browser can let them select the host they want. It should have 3 (or more) distinct modes of operation: Gossip, where popular portions of the zone are continually shared between nodes; P2P, where queries traverse a graph of peers, rather than a tree; and a Classic mode, which functions as DNS does.
I want a standard way for ALL OSes (incl. Mobile) to share notifications. I can't even get my phone and smartwatch to share all the notifications I need, and they're from the same manufacturer!
I want a protocol and software to combine the paradigms of Syncthing and FTP, so you could download a folder's contents (or a subset thereof), or keep it up to date, all with syncthing's discovery and authentication framework.
I want a platform where every action is entirely scriptable in something that's not Javascript. Get an IRC message while I'm not there? Send the text to program A. New USB device inserted? Launch a virus scanner there. It would be exceedingly helpful if you could tie in to the browser and define scripting events on 3rd party pages.
Finally, I wish Plan 9 was a viable desktop OS because its protocols and paradigms line up very nicely with some of these. Plus, it's a really neat, simple OS.