Ok, so all I really can remember about this movie is that there is some kind of king with a very powerful rod and he gets taken by the black cloud and is imprisoned in this black goo or something, and I remember a little boy that rides on a toy train in the beginning. Please help me if you can!

Pretty sure the lad in question is our old friend Little Nemo, as you will see in the detailed write-up by my esteemed colleague Stardust713:

https://www.askmehelpdesk.com/movies/animated-movie-name-124927.html?highlight=nemo+goo