If you mean real stock agencies then you will likely be working on a contract so the answer would be no. If you mean pretend internet agencies then you can do what you like.
they arent "pretend" stock agencies, they're just a different type, they still have lots of photos getting sold, but the one HUGE difference, is that on a microstock, you ususally dont make much. for example, a while back i put some photos on istockphoto and have sold maybe 5 of them and have made under a dollar for each one... in my opinion, in less you have hundreds of very good stock images, its not really worth your time
There are some stock companies out there that really work with their suppliers and will even connect photographers directly with clients so that clients get exactly what they want. I have a list of some somewhere in my office. I will have to find it to let you know what they are.