I hope YC does something like this again in the future, but I'd suggest a different approach: Rather than asking HN to help select startups to fund, I'd suggest asking HN to help select startups to interview. This would solve the problem of needing an out-of-band mechanism to determine if an application is "real" or not; worst case, YC would end up paying travel expenses for some companies they decide not to fund. I suspect that the advantage of having extra eyeballs ensure that they don't overlook promising startups[4] would easily justify this -- not to mention the possibility of saving YC lots of time on in-house reviewing.
The one biggest danger I see with this is the potential for vote brigading; I suspect that we would have had more of that if it was announced at the start that votes would be a significant deciding factor. One possible way of solving this would be to limit voting choices, e.g., ask each person to pick one out of a small subset, so who only turn up because they want to support a particular candidate would usually end up filtering themselves out. I suggested this to Dan, but he thought that there wouldn't be enough voters to make this feasible; I'm not sure I agree with him.
Obviously I have no idea how this experiment is being viewed from YC's perspective -- and it sounds like YC won't know how they view it for a while yet either -- but as an external observer I'd say that this was a very interesting and very successful experiment.
[1] I'm sure that most people who voted for pinboard did not do so because they thought it would be a good investment. This gets back to the "it's not really clear what YC is trying to accomplish with YC Fellowships" problem which I've mentioned in earlier threads, but the original call was to "fund startups", not "fund your friends".
[2] I think that YC could gain a lot by creating some other mechanism to bring people like Maciej into the system -- something like an "honorary YC founder" status. But I don't think funding is the answer here.
[3] I'm a Canadian and not particularly familiar with the US legal system; but I've seen enough of it to know that (a) there's a huge amount of money there, and (b) they desperately need an infusion of technological competence.
[4] I'd be interested to know if any of the three had applied to YC via the normal route: Did HN identify good startups which YC missed, or would YC have funded these three anyway?