Welcome, one and all. After much deliberation and more than a little fretting, two victors have emerged. There were quite a few entries, and more than enough to keep me second guessing myself. Many of them were excellent, and simply choosing two of them was a hugely problematic task.
To those of you who entered and aren't named "CloudySkies", this next bit may come as somewhat of a relief. Cloudy was invaluable and much appreciated during the judging, both for opinions and as a wall to bounce things off. It's fair to say that without him this contest probably wouldn't have been judged until January. Of course, he also *entered*, and we both felt that this perhaps caused a conflict of interests. As such, No Recipe For Perfection was not in the running, but you should go read it anyway--it's a fantastic story.
Secondary special thanks goes to kits, for some opinions and, more importantly, moral support throughout.
Before I reveal the victors I'd just like to make clear my biases and criteria for victory. I care about technical quality, but not as much as concept and heart. A great story written poorly beats out a poor story written perfectly every time, for me. As such, judgement here isn't necessarily a reflection on the technical ability of the writer. I am hugely biased towards cute ponies being cute, and that's what this contest was all about. I'm unashamed in saying that it's the characters that draw me to shipping--I love seeing a character I empathise with happy. This doesn't rule out non-main cast members, and doesn't even rule out OCs, but it does put both at a disadvantage. A very very personal bias is that I'd also rather give light to a lesser known author than a more known author, all else being equal.
So, with no further ado, here we go.
First place goes to:

Stubborn as Ponies by Esle Ynopemos
A pony is called stubborn when they refuse to change their mind no matter the persuasion against them. A pony is called persistent in hindsight when their refusal turns out to be a wise decision. "Persistence" is nothing more than what they call stubbornness when it turns out to have been for the best all along. Pinkie Pie and Applejack may or may not be persistent, but they are most definitely stubborn.
I loved this one, I really did. Like no other entry it really captured the spirit of the contest, and was very well written to boot. This one I had little trouble deciding on, because with this one story the entire contest was justified. ApplePie is an adorable but underappreciated ship, and this story brought out why. Perhaps a mite unprofessionally of me, I couldn't help but break official silence on this one and suggest the author submit it to Equestria Daily.
Basically, everybody go read this, and then go follow the author. 120 watchers is a little bit criminally low, there.
Second place goes to:

In Search Of Knowledge by thehalfelf
On a normal weekend, Cheerilee assigns everypony an assignment she had been giving for years, to tell why each type of pony is different than the others, and how they can work together. However, Cheerilee finds out the book is old, and Twilight offers to help her rewrite it. Along the way, however, some things may be learned that aren't exactly in the curriculum.
This one was a much harder decision. There were a lot of contenders, and anybody who's read them all may be a little surprised at my choice here. As I said above, my biases are clear. Yes, this story has issues. A lot of the characterisation is a bit off, especially with secondary characters. Grammar is a bit iffy and conversations often resemble a telephone call due to the lack of body language. Word repetition is often jarring, as well.
Problematic execution can be fixed by a good editor and a close eye. Problematic concepts or ideas won't shine through no matter how perfect the execution is. That's why this is here: Yes, it has some problems, but the important bit--the romance at its heart--shines through strongly. So long as the technical framework that holds a story up is good enough, then it can be enjoyable, and here it is well above "good enough", just not quite into the realms of "flawless".
Here, the ship carries the rest, and it does it well. It's an adorable, well paced progression that doesn't make it too easy, but also doesn't drag it out. As a short feel-good piece, it excels. Everybody should go read it right now.
Finally, a closing personal note. Thank you all very much for taking part, I appreciate the chance to bring some good out in this community for once. I wish every one of you the best. You all deserve it. <3
A side note, I probably won't be around much over Christmas. As my primary internet enabled device away from home is my trusty Galaxy S3, and fimfiction appears to take every opportunity to make itself unusable on a touch screen, I won't have a great deal of access. I am not buying a bluetooth mouse just to work around poor design.
Merry Christmas and a Happy New Year, everybody!
-TAW