Just like with cakes, a simple syrup will keep a cupcake moist longer.
Also, I have found that cupcakes made with buttermilk and oil (versus butter) tend to produce the moistest cupcakes.
At the cafe where I work, I always make batches of cupcakes and freeze them. When defrosted, they seem to sometimes be even moister (and stay moist) than when freshly-baked.
Also, if the cupcake your baking tends to have a "crisper" top (some cupcakes tend to have a crisper top than others), then brushing simple syrup over the top might not penetrate the cake below. In that case, I would think that you could use one of those food syringes and squirt some flavored syrup into the cupcake.