AI find that my cupcakes are never as moist as my cakes, even when I use the same recipe. I know I'm not over-baking. Should I be using a different recipe for cupcakes?

Yes, cupcake and cake recipes are interchangeable. It's very easy to overbake cupcakes without realizing it because they are so small compared to a larger cake, 

.all of *my* recipes are...but there are some cupcake recipes that suck as cake recipes and need to be tweaked.

AI've been fairly successful with interchange between both but I highly recommend reducing bake temp by 10 degrees or so and watching around the 11 minute mark. HTH

Usually they are, but not always. I have a few cake recipes that cannot be made into cupcakes, but they are pretty complex.

Cupcakes only take a minute to over bake, I actually take mine out a hair before they are finished, and the residual heat finishes them off.

What temp are you baking them at? I agree with daisy, reducing the temperature is a good idea.