Thousands of magazines and websites publish short stories. Submitting to all of them would be expensive, time-consuming and futile. You must narrow the field and send your story to the publications that are most likely to publish it. In other words, you have to find a "fit."
First of all, if this is your first time submitting a story for publication, you probably want to stick to smaller magazines or those that specifically try to help out novice writers.
Next, decide if you want to make money from getting the story published. If so, good luck: Even many of the most highly respected literary journals won't pay for stories. To make serious cash, shoot for big, glossy publications with a hefty bankroll, or work towards publishing a collection of your own short stories. However, for your first short story, you should really just be satisfied with getting it published in an unpaid journal.
Also consider whether or not it is crucial to see your story printed on paper. If not, online literary sites might be your best bet. There are a lot of them, and it still counts as a legitimate publication. The downside is that there's no guarantee the story will get read. But is it crucial that a lot of people read your story? Again, there are a number of small journals with circulations in the dozens that may publish your story if you're not particularly worried about being known to readers coast-to-coast.
Does your story have a particular ideological/cultural background others may identify with? This is the question many first-time writers forget to think about. There are dozens of magazines out there for all conceivable ethnic, cultural and religious groups, as well as lifestyle magazines for people with particular hobbies or occupations and magazines for specific geographic regions. Figure out the target audience for your story and you'll improve your chances of catching an appropriate editor's eye.
You should also consider paying to have your story read. There are hundreds of short-fiction contests across the country with prizes ranging anywhere from $50 to a couple thousand dollars. If you think your story can win, shell out the $10 to $15 per entry. Just make sure the contests are reputable. Find out who last year's winners were, and make sure these are real people, and that your story will get read. Many smaller magazines also have required reading fees, but every submitter gets a free subscription to the magazine. If you're interested in reading short stories as well as writing them, this is a good way to feel like you're not getting bilked out of your reading fees.
Finally, think about any of your connections that might be able to help you. This doesn't just apply to you if your dad edits "Harper's." Almost every college and most towns have a literary magazine, and if you're interested in being published, you might want to get to know some editors. They'll be able to give you inside tips on what the magazine is looking for, and if they like you they'll probably read your stuff first.
