
I don't really have the time or the inclination to write a lengthy and deep post right now, so I'll just resort to a more filler type of post, concentrating on the shallower aspect of this blog. Well, it's not like this blog ever pretended to be anything other than shallow, sesquipedalianism notwithstanding.
Appearances play a major part in determining whether a character will induce that fanboyish reaction of moe~ upon clapping eyes on the character design, but exactly which aspects of appearance will engender the right reaction varies greatly from person to person. Some people like long hair, and some people prefer boyish cuts. Some people like dark-haired girls, while others go for blondes. Some people go gaga over maid costumes, while to others, a catgirl outfit is the pinnacle of cute.
As such, I cannot and do not pretend to speak for anyone else during the course of this entry. Everything listed here are my own interpretations and ideas and opinions, which I do not believe are shared with anyone else in exactly the same way, even if I'd be happy if some, or perhaps most, of the points strike a chord with other people.
I will understand, however, if nobody else shares my tastes. I am perfectly content to identify myself as being completely and utterly moe for meganekko, the girl with glasses.

And in one decisive blow, Kyon crushes the dreams of anyone who shares my taste in moe. Well, not crush, perhaps; more like a minor setback, and the existence of Yuki fanart with glasses has renewed my faith that I am not alone. Besides, there's always the infamous Volume 4 of the novels.
Besides, Kyon is also moe for ponytails, so he can probably understand where we are coming from.
Why do glasses seem to increase the attractiveness and moe factor of a girl? Answering this question may be as hard as answering "why is the colour blue?" It just is, or does. We can break it down into individual components and analyze them all to exhaustion, but in the end, it really all depends on Personal Taste.
Still, I need to write something here, and something I shall write.
One possibility is the aesthetic framing of the eyes. The more moe character designs tend to have large and expressive eyes, and having glasses brings this out much more. The eyes are both seen, since the glasses are transparent, and yet obscured, since we do not actually see the eyes as they are, but through a lens, just as the character looks at us from the other side. This is demonstrated with the typical "glasses-glint", where the character tilts their glasses at a certain angle to reflect the light off them, hiding their eyes. This is usually seen to be particularly menacing, and I would say that it's not just an anime trait; people tend to get nervous around those who wear shades. They invariably appear to bear secrets, possibly unpleasant ones. (In many anime, when a character momentarily gives in to their Dark Side, their eyes may get hidden under their bangs.)
It may be that combination of being both open (and thus honest) and closed (and thus mysterious) that makes the girl with glasses seem more intriguing than her companions.

Another factor dives into the realm of fantasy, or at least fantasizing: the thought of meeting and being close to the character with the glasses, and earning her trust enough to take her glasses off. The girl blinks in confusion as her eyes adjust, and is, for that briefest of moments, vulnerable and in need of protection from the things she cannot see. And isn't the concept of protection a core part of moe?
This doesn't always apply to every situation, of course. When the girl takes off her glasses herself, assuming she's not doing it to clean them or to go to sleep or something, she invariably does it to be Dramatic and Confident. This is not, in fact, a bad thing, since it may provide for moments of bravery that should be cheered on and emulated. (Or, in more comedic anime, moments of stupidity that can be commiserated with). And if the glasses are knocked off by an unexpected violent force, that probably means that Something Is Happening.
And then there's the feel, thoroughly illogical and completely shallow, that having glasses would mean that one is smart, or at least well-read. This would translate into a sizeable INT score, without any regard for the WIS score; the classic example of high INT and low WIS is the absent-minded professor, and translated to a moe female character, we get Yomiko Readman from Read Or Die, one of the most attractive characters I've ever seen in any medium. Not merely good-looking, but also fascinating with a combination of her cheery, optimistic, gentle personality, as well as her love of books.
Of course, the assumption that a meganekko is well-read plays on character stereotypes, but with the aforementioned Yomiko Readman, as well as Naoko Yanagisawa (Card Captor Sakura), Li Kohran (Sakura Wars), Fuu Hououji (Magic Knight Rayearth), Ami Mizuno (Sailor Moon), and certainly Yuki Nagato (The Melancholy of Haruhi Suzumiya), it is not without some basis.

Finally (at least for now), somewhat related to the previous point, a girl wearing glasses may well be more attractive to a guy wearing glasses, simply because she would count as One Of Us, in some small way. We can identify with at least the part of the character that has to periodically take off their glasses to give them a wipe, or have to be particularly careful with impacts to the face in case there is an unexpected shatter.
Overall, as mentioned at the beginning, there is no real definitive answer about why meganekko can be attractive. In fact, it's not even that glasses alone can make the moe, but more that glasses can enhance what is already there. In almost all cases, I can rattle off a huge list of other reasons why the character in question is to be adored, and the addition of a pair of glasses just provides the finishing blow to reduce one to a puddle of hanyaa~n.
I do have to mention that every time a cute girl with glasses decides to switch to contacts, I feel a tiny little twinge of sadness inside.

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That first pic of the Sakura meganekko… sweet lord that's
hawtadorable.Personally the Sakura meganekko picture doesn't quite resonate with me, maybe because I'm used to non-glasses Sakura, or perhaps that her character doesn't quite fit the meganekko standard, no?
I think that meganekkos overlap a lot with the quiet moe that you posted about earlier, which is why I'm an admitted megaquietnekko addict ^^ The ones with glasses (because I'm tired of typing meganekko now) tend to be the ones that are shy, easily embarrassed, the protectable type (see Miyuki above, cue moe-ness), or maybe the strong and silent (Nagato's the obvious choice here). Both examples being incredibly adorable and awesome. And that's why I'm a glasses girl fan, at least, because 99% of the time you're on the road to someone really likable to a fanboy like me.
Sakura, being none of those but rather more of the Genki Girl, to blatantly use trope names, just doesn't seem to click with glasses. It's rare you see her that reserved, with that shy little smile.
Now, how about some Mai Kawasumi in glasses, no? :D
-CCY