What a long and strange journey that was. Even more than the novels reading the Hugo winning short stories really gives on a cross section of science fiction from the 1950's on. From the light pulp stories that began it to the psychedelic New Wave to the refinement of the literary form that followed to the fragmentation of subgenres to the fading of science fiction in favor of fantasy; the award winning stories are SF in microcosm.
Looking back through the list of winners by my count I enjoyed a bit more than 60% of the winners. I don't think that's a particularly bad average given the standards I hold the stories to.
By a few arbitrary categories:
Best Story - There really isn't any other choice than Daniel Keyes's "Flowers for Algernon" which won in 1960. Not only a great story, it's acknowledged as one of the most significant short stories of the twentieth century. It's one of the stories that you can point to in order to demonstrate the significance of science fiction.
Worst Story - It's hard to select one but I have to go with "Down in the Bottomlands" by Harry Turtledove which narrowly defeats the moral bludgeoning of Ursala Le Guin's "The Word for Wold is Forst" and the goofy superhuman story of Orson Scott Card's "Eye for Eye". As bad as those other two were they lacked a character named "Evilla" whose defining characteristic was that they were evil.
Author Who I Never Want to Read Again - In my life I have read five stories by Jon Varley and of those five of them present pedophilia as a positive thing that is beneficial for everyone involved. Even in a novella that didn't involve children he managed to work it in as part of the back story. It's enough that I now considder Varley's name a warning to avoid the story.
Author Who I'll Read Whatever They Write - A much harder decision since there are three current authors whose short stories have convinced me that I'll want to read whatever they put down on the page. For quality and consistancy based solely on their Hugo winners I have to go with Ted Chiang who narrowly beats Connie Willis (who is consistantly enjoyable but tents to alternate flippant nothings with more deep stories) and Michael Resnick (who is great at presenting morally ambiguous stories). Chiang beats them because of his ability as a literary chameleon, able to shift form to always given the perfect presentation to his concepts.