I'm not going to make myself very popular, but so be it...
I'm not fond of the idea.
Please lemme explain.
First off, there's the localization problem. There's usually no point in showing Europeans missing American children or vice versa (I'll get to the exceptions). Or even above...say...a 300km radius of the previous home (and that depends on how populated the area is). That means that it's not just that webmasters should just slap some 'missing' pictures on their site...they will have to allow the NotFound project to check the location of the 404-ing person and use that to show a local picture on their website (well, okay, not exactly website, but...you know what I mean). Fun...those surfers who block their location are out of the loop (well...unless they don't mind getting a picture of someone missing on the other end of the globe).
Since it's only really useful on large sites, that means it'll be an extra security/reputation issue. I can already hear wannabe hackers making bets on whether they can get a lolcat picture on a 404-page of a major site. It'll be out of control of the webmaster of that site...but he will get the flak for it nonetheless (been there, done that, didn't like the T-shirt).
Not counting that...just how successful was that whole "photo on milk carbon" thing anyway? My bet: not very. I sometimes see pictures of missing people in the train station, and I can tell you this: I wouldn't recognize the person if he or she was standing directly next to it with a big purple arrow above. The reason: I don't expect to see that guy. Honestly...that beggar I pass on the street could be Bill Gates or Reggie Fils-Aime (when not in fancy suit, obviously), or no matter who. They're out of my field of attention. On my way to work and back, I can wade through entire hordes of people and not see anyone. And I'm not the only one: we all do it. And with good reason: in any urban area, the chances of actually seeing that someone is about as close as winning the lottery.
But...it could still help, right? Sorry...wrong. I bet that from all those missing children, the police gets at least a dozen calls from people who are cocksure they've seen that person...and who are plain wrong. This sort of search creates a lot of work for a lot of people (mainly police and detectives) that results in little to nothing.
And it gets worse. Think about it: why does a child goes missing in the first place? Many reasons. Let's take things from the least to the most likely of them:
* child rapist/murderer/scum. They exist. But even just looking among missing children, these are the least likely cause. But even then: it's not as if you're "just" going to find them by a picture. Gruesome as the details may be, spreading a picture around isn't going to actually help.
* child lost its way home. Sooner or later, he or she will either find back the home, and if nothing else the police.
* the child's running away from home. Okay...and why does the child does this in the first place? Like it or not, but teens WILL revolt against their parents at some point. They'll run off, do some stupid things teen do (to those above 25: we were young too, right?), find out they're not as mature as they thought they were and return home. Hopefully not pregnant in an anti-abortus state.

* abduction by one of the parents. Marriage and splitting up is a wonderful thing, isn't it? You suddenly have to split up everything. And while chainsaws aren't allowed, the real life result sometimes isn't THAT less frightening. I've heard more than one tale where desperate parents had almost no other option but to abduct their own child because the former other half was a bitch or bastard about it.
Even more fun if different countries are involved: the child is glad of the long vacation (erm...at the start, at least) and plain out trusts the abductor. Probably for good reason.
Taken all combined...aside from the murderer option...I really don't want to get involved. I have known a few people who ran away when they were kids, and they're both more mature than the average people I know (probably exactly because of that). I've also known people who lived in...how to say it in English? ...empty houses...dens? Whatever the name...they were BY FAR more free in who they were than the average Joe.
I don't want to sound like an old fart preaching from "1984", but c'mon...have you guys never thought that those people on the pictures could very well be somewhere where they WANTED to be?
That's also the final reason why I disagree on the idea: it makes the world look like an insecure place. It's as if the whole world is somehow "wrong" because a child is not where he or she is supposed to be: constantly supervised by parents and getting worked at school to fit in that model that can withstand the ratrace of a boring routine in a world that holds no secrets.