That's a case of black knot in your cherry tree. Black knot is a fungus that affects both cherries and plums. The galls eventually girdle the twig and kill the growth beyond. It can also get onto the stem and cause more serious damage. If you want to, you can prune out the infected branches, or cull out heavily infested trees. Some cherries are more apt to get it than others, and often when you prune it out, it comes back since the tree is susceptible.
Prune them out now (before bud break). You can leave them to rot, since it is common. Or, burn/bury them to help prevent reinfestation (more important in nurseries and orchards).
A good reference: http://ohioline.osu.edu/hyg-fact/3000/pdf/HYG_3011_08.pdf
These is black knot of cherry. Very common in young trees. That's a pretty bad case of it you got there. The only way to get rid of it is to cut it and burn it. However, it is very common and the trees usually survive past it.