With fall, I would think that there would be plenty of stories to mention the fall harvest and that sort of angle. Plenty of them do mention the harvest briefly, but it usually doesn't seem to form the center of a story for the simple reason that the fall harvest is a good time and stories need conflict in order to have any sort of plot. So it's more common for stories to have an overall sense of the decay and overall windiness of fall than of the bounty of the harvest. At random, I've chosen three titles to touch on today.
"The Fall of the House of Usher" by Edgar Allan Poe. I mentioned decay, so naturally I was thinking of this story. It's all about decay: the decay of the house and the decay of the people in it and the decay of the family in general. For a dark look at fall, this is the story. Since it's Poe, it naturally also ties in well with Halloween. More, though, than the "spooky" elements of the story, it's the elements of nature that he describes that make this story fit in so well with the atmosphere of a season of the weather.
Silas Marner by George Eliot. I don't remember if this short book focuses in particular on any one season. But the overall feel of it has always made me think of fall. Silas Marner is, in many ways, at the autumn of his life. He is no longer young and he has nothing to make him look forward to the next day--and when he loses his gold, he loses all his happiness. Yet he finds a new kind of gold in the form of a gold-haired child who falls into his lap and becomes a daughter to him. The color gold, simply, is reminiscent of autumn because it's the color that many green leaves turn. And the sense of the old that will soon be replaced by the young is very much like the changing seasons: the blooms and green grasses and leaves fall and fade away in autumn to make way for fresh ones to come in spring.
Wuthering Heights by Emily Bronte. Probably this book has more of winter in it than spring, but it feels more like fall. There is so much talk about the wind and the isolation and the moors and the wind, all of these harsher elements of weather. And then there is Heathcliff. He is Nature, this inexplicable and unstoppable force, this harsh element of weather that rushes in and takes over for a season before fading away again. He's too alive to be winter; instead, I think of him as fall (winter is his death). Here is a combination of the previous two titles in the sense of darkness and seasons that will change.
From a daily perspective, no, I don't think of fall itself as dark. It's an exciting time, when the weather cools off enough to start going outside again more often (or at more times of the day). While the wildflowers of spring are beautiful, so can be the dry grasses of autumn. And with the holidays coming up, you start getting a nesting feeling that takes you into the short days of December. So, no, I don't think of fall as dark; it's just that there are some wonderful dark elements to books that focus on the changing of seasons.