Idiot proof?
You'll just find an ever-more-ingenious way to idiot things up!

Yeah, I've been there.
(Example, crossing the wires after the protection; forgetting to install the protector circuit; etc.)
That said, what kinds of solutions would be most likely to be followed?
The simplest may be using a carefully current-limited supply. You'll get good regulation, and stable current limiting, with a standard constant current source circuit; putting two, back to back, also gets overvoltage protection (say, cross-wiring the 12V supply to the 3V rail), and doing it on the ground (if it's wired separately from the other supplies) also gets you polarity protection. If you don't mind buying parts you probably don't have on hand already -- a few depletion mode MOSFETs does this nicely, and are available to over 200V and a few watts dissipation (almost good enough you could cross-wire mains to the poor thing!).
Limiting the current to a few 10s of mA, and not placing a large capacitor on the supply's output, allows the possibility of survival, even if you cross-wire that circuit to VCC or an IO pin. If more current is needed, you simply don't have any way to assure that, and you'll have to box things up and protect all the wires entering and exiting that box.
Example, using a dev kit with MCU onboard, and protection wired up to all the pins. Maybe clamp diodes, so excess voltage/current gets dumped into the supply, then the supply itself can be protected with a TVS (if ~5V) or crowbar (if less).
Incidentally, even if lower voltage TVS diodes are available, they really don't perform any better than 5V parts. To get guaranteed low clamping (like 4.0V for a 3.3V supply -- a lot of 3.3V parts catch fire in the 3.6 to 4.4V range), you need to use an active circuit, potentially with fast response time and very high current capacity (in the event you wire a charged capacitor across it, say -- a 1000uF electrolytic will easily deliver 100A short circuit!). This is a surprisingly challenging problem. More often, a latching circuit is used (namely, an SCR -- see above examples), in which case the supply stays shorted until current is removed.
Tim