I am not the right person to answer this.  I've played there but once.  Several others are way way way more familiar with the course than I am.

Nevertheless, I do see greatness in those golf holes, or at least three out of the four.  Of course this is gonna turn on how one defines "great."  I shall explain.

#3 - it really is one hell of a great golf hole and it goes far beyond what you say.  The green isn't a simple back to front slope, but rather has shoulders off the bunkers and other more subtle breaks, making it just a monster to putt.  Also miss it and any chip/pitch is going to be very, very tough.  Playing as long as it does, it just falls into such a brutally tough category that I believe that, combined with the history there (Casper laying up, etc.) is enough to connote greatness.  

#7 - what you're missing is that the green is very raised - it's a strange shot in a course otherwised filled with greens more flat to the land.  It's also a rare short approach shot on that course, and you expect it to be easy... but then you are zinged.  Perhaps tough to call it "great" in the world-class context, but nevertheless it is a fun, tricky, surprisingly tough golf hole.  I like it a lot.

#10 - enough has been written on this, not much for me to add.  I have posted here ad nauseam that I don't see the world-class greatness - I was underwhelmed playing it and I do think 3 is a better golf hole - but even I admit the green is freakin' brilliant.  Others can add more, hopefully.

#13 - I didn't see much greatness there either.

So 3 out of 4 are very, very good golf holes.  If one wants to say each is world-class great, the argument is easy against that, I think.  But 3 and 10 each come very very close, if not actually meet the standard.  Then you think of them as a group, and well... the list of courses with par threes as a group better than WF-W would be short indeed.

TH

Challenging ,but other than #10, not great.

The  sets at  Newport ,Myopia Prairie Dunes,  and Franklin Hills, exude greatness due to thier varied topgraphy and charm

Ironically WFE #6,13, abd 17 are some of the best  on the whole property..... WFE par 3s are outstanding

Matt,
   You have played at Prairie Dunes right? What makes #2 a great par 3? I would say given three uphill shots out of 4 to greens benched into a dune ridge shows a lack of variety at PD but each par 3 is challenging in its own right. #10 is a bit of a different setting, but is a challenging tee shot, with probably the least interesting green of the set. Tell me what you think about the par 3's at PD and perhaps I can help you understand the par 3's at WFW. However, in my walkthrough of the back nine last fall #10 was the one that jumped out at me as truly inspired. Think of #6 green PD-type inspired.

Matt,
As Tom Huckaby has indicated, it's really all about the green contours and  how they present themselves at attacking them from the tee. And one can't forget of course, the bunkers which sort of pinch the entry and leave no room for error.  You could play long, but Tillie wisely gets you there too, because if you are long, then you have these built up from the back drop offs, which he ingeniously shaped into the somewhat leel entrances.

Trying to describe it better, and Coore & Crenshaw build many of their green complexes in the same way--I compare it to like being backstage in an old theater where you see all of the essential stuff that goes into making the audience see the set. Behind that set is a quanity of ropes and stancions that support these massive sets.

With Tillie, imagine that being done all on the ground with shaping of the earth. It's sort of raw to see the back of a Tillie green complex, but it allows you to see how he masterfully created these maginificent contours of the green complexes themselves. The back of the green supports much of the flow and direction and how the green itself provides the strategy from the tee on each and every hole at Winged Foot.

I feel the par 3's really do benefit from all of it.

I hope that make sense.

I believe the simple answer is the green complexes.  If you execute the shot as required then perhaps they are like any other par 3's.  The brilliant features, however, apply to how different less then excellent tee shots are penalized. Certain pin locations will absolutely reject misses in the incorrect places and "safe plays" away from pins frequently result in what one member likes to demonstrate to his guests as "challenge putts" that are VERY difficult. Once you come to realize the precise play required at each hole it makes the resulting shot that much more difficult.

Geoffrey nailed it on the head. Most great holes, or at least great greens which IS the hole in the case of par 3's, have what Dr. Childs points out in his last sentence.

We were struck by how much of Winged Foot's overall distinctiveness doesn't come across on TV. I brought some people to walk around, just so they could see the green complexes and have a full appreciation for what the pros are up against when they watched later in the week on TV. We were also remarking to one another what an incredible group of par 3s these are. The yardages vary. The complexes are amazing, and make sense for the yardages. As good a set of parkland par 3s as one will find.