One-Shots:
I have probably reread My True Feelings a hundred times. It's adorable, it's heartwarming, just a right balance of angst and fluff, and it has great, true-to-source artwork. I'm not the biggest Yuru Yuri fan, but this doujin converted me to a ship I'd barely even considered. Just so damn good.
Similarly is Talk of Little Love. Aki Eda's artstyle is just so damn adorable, and it makes this doujin all the cuter and sweeter. Yukari is the best character.
My True Feelings would be my pick if you asked me for my favorite one-shot; but if you asked me what I think the best one is, based on pure, objective quality, my pick would be Jewels. The art, the writing, the plot, the characters, everything just comes together in an incredibly satisfactory way to make one of the sweetest, most fulfilling one shots I have ever read.
Another Aki Eda piece, Plastic Heart is a good one when I want a slightly longer read; the doujin goes on long enough to squeeze out a great amount of comedy, angst, fluff, and sweet, fluffy feelings, but it's not so long as to feel like it drags on. Plus, that kiss!
The Long Wait is Over is a great one primarily for the viewpoint character; Yano's snarky inner monologue mixes greatly with SAD's trademark translation style, and makes it a very humorous, satisfying read.
From Aiu Station on the Hiragana Line and I'll Send Her Home on the Last Train have S+ tier relationship progression and a supposed gold-digger protagonist who just needed the proper motivator to realize how gay she really is. What's not to love?
Dusk, Orange, The Blooming Flowers... is my favorite pure drama/angst story. It manages to be realistically dramatic without being too heavy-handed, and I was sad about the ending, but not upset about it; rather than being unsatisfied, I just felt bad. It moved me enough that I just knew I had to include it here.
Damn, this ended up being a lot longer than I intended. I'll do something else for series at another point.