There are a few established shops/stalls but they're mostly in the major settlements/cities, like Diamond City (though there are a couple of exceptions to that). The rest are traveling merchants that you'll periodically run into in your travels. Some of them will also visit certain settlements that you establish/build, like Sanctuary.
If you get into the settlement building/management part (which is almost a game by itself), you can also build your own shops and assign settlers to run them.
Another good use for all the extra weapons & armor pieces you pick up, is to equip your settlers so they can better defend the settlements. When they initially show up, the usually have no armor and have a crummy pipe pistol or pipe rifle. They'll get chewed to pieces in an attack if you don't upgrade their equipment.