Once you can do your own processors, the architecture is alright. To avoid running into licensing issues all the time, projects like RISC-V (http://riscv.org/) can help - or open cores like Leon (SPARCv8), OpenSPARC-T1/2 (SPARCv9), openRISC and several more.
The problem is, the silicon processes were optimized for investment heavy, large scale operations. To ensure the livelihood of general purpose computing we need a "3D printer for logic gates" (for lack of better term), even if it's economically and technologically less efficient (but not too much, obviously).
EDIT : Also, HomeCMOS doesn't look active as of June 2013.
For the higher software stack, Linux on RISC-V already exists, and from there it's open source, a compiler plus some portability work to get a useful stack.
But that's only the CPU side. Good enough for embedded applications and maybe even servers - but at some point, data has to hit a display. http://www.miaowgpu.org/ or something like that could help there, but I know next to nothing about it.
Take this with a grain of salt because my exposure is admittedly limited, but what I've seen of the "research community" is that many of them are pro-DRM, pro-anti-user-security, and are mainly interested in furthering such technologies without considering the wider implications. I once asked someone with a vision of making all systems written with formally-verified provably safe languages what he thought of jailbreaks, console homebrew, and all the other exploits that bring freedom. His response was that they shouldn't exist.
I'm not really pleased with what Intel has been doing with x86 recently, but fortunately it wasn't always that way and a huge amount of software and documentation was created during that time so we don't have to start from nothing at all. IBM released schematics and BIOS listings for all the models of PC up to the AT. Thus it could be better to "fork the PC"; but individuals have designed and built their own CPUs and complete systems before, so a from-scratch design is still quite doable for a crowd:
Jail breaks are always a stop-gap measure, since they're quite obvious against the interest of the system designer, and so they'll work on plugging the holes.
At some point they will develop the safe methods themselves, and if we "shun" public work in that area, only jails will be safe, not the open spaces - which, among many other things, would be a PR nightmare for general purpose computing (Example: Apple and their "safe", filtered appstore).
x86 (and _64) and even ARM are all primarily developed by govt-influenced companies like Intel, yes? So what are the possibilities of us, all programmers and electronic engineers who want to support personal computing, to get together and develop a crowd-researched, crowd-designed, and (maybe) crowd-funded architecture to last the future. Of course, writing software for that architecture could take decades-centures (unless someone writes a perfect x86 emulation layer on that architecture), but at least that gives us a hope for the future, a backup to fall to if Intel pulls a full on 'google' on us.
So are these just big dreams or is there an actual possibility of something like this happening? Especially if the community secures the funding of some visionary who's rich as Bill Gates (maybe the man himself) and on the side of the public? That way we'll be able to actually build a system from the ground up that is libre and transparent, without having to muck about with reverse engineering on the 'enemy's ground', so to speak, like corebook does.