OK, here's an idea. I imagine you've all seen copiers with multiple output "slots," right? OK, attach that to an optical-scan reader. As the ballots feed in, the machine puts (say) the Obama ballots in slot 1, McCain in 2, Baldwin in 3, Barr in 4, etc. Once it's gone through the stack, you apply a hand-count of each pile to do two things: (alpha) verify the actual quantity (the machine would keep its own tally, and while the hand-count should be primary, more than a certain discrepancy from the machine count would trigger a double-check), and (beta) make sure the ballots in each pile really are marked for the candidate whose pile they're in. Repeat for each race/proposition on the ballot. (Vote-for-more-than-one races are trickier, because of the exponential number of combinations; one pass per candidate might be needed).
The biggest concern there would be that the machine itself was "disappearing" or mangling ballots. Transparency in that respect would be achieved by literal transparency of the sorting machine.
