Subete wa Maguro no Tame datta by Boichi, from the Hotel one shot collection. Boichi is better known for ecchi martial arts manga Sun Ken Rock, but Subete wa Maguro no Tame datta is a humorous, intelligent, "Hitchhiker's Guide to the Galaxy" inspired story about protecting the environment. The entire Hotel collection is outstanding, particularly the title story.
Koe no Katachi's one shot is currently what at the top of my head right now as a recent One-Shot. I remember it was beautiful to read, but I am kinda skeptic when it becomes a serialization, so I haven't read it yet.
I read DRUMP in 2013 so I will definitely include that on my list as one of the best jump one shots in awhile. The best friend Nero design may have been lacking but that didnt hold this back from being a really compelling and even suspenseful and thrilling series for its 50 or so pages. I wish it did extend to a full series as the DRUMP game is actually kind of fun and interesting and makes me wish to play it, like those DRUMP players and videos going around on jpn mangatwitter. A game being extended from a standard deck of cards and still seemingly potentially as complex as modern cardgames from bushiroad and konami raised it a few bars in my book. I enjoyed it and the visuals and the facedown with bursting.
Death Note pilot: I think it was a tad better than the series. I don't know... maybe it's because you have kids using it instead of mature adults.
In the Chocolate: Nice romance story.
Jump Super Stars: A jump crossover manga that's not fan-made.
Koi No Kami-Sama: Talk about bad luck...!
Magic Bloomers: Simple, but funny.
Tokyo Photograph: Another nice romance story.
Watashi no Mahoutsukai: So is this.
Stray Dog: It made me shed manly tears!
I still remember reading Kaiten!! by Hoshino Katsura in 2011. I was really impressed with it because it had a plus-size female lead who had super-human strength. I kind of wish Hoshino would go back to it after finishing DGM (we'll see how that goes). There was something about the heroine that was really bubbly.
Another one shot I enjoyed was Hanasaku Ikkyuu....I liked it much better as a one-shot than I did as a serialization.