Choose one or two colors for the walls that will compliment the boys bedding set that you have chosen. One color should be more neutral for the majority of the space. The second should be a deeper accent color. An example would be if you have a surf theme toddler boy bedding set, you could use a pale blue for the main areas and a deep navy for the accent wall.
Shelving and Storage
It's always nice to find shelves or storage units that match the theme of your boys room. An example would be buying silver metal look shelves for a very modern or electronic style room. Or classic white for a nautical space. For complimenting a boys bedding set that is either characters or something like dinosaurs, you could paint a wooden shelf or bookcase in a complimenting color and then look for bookends that are dinosaurs.
Baskets Baskets Baskets.......
There is always room for one more basket. Most popular for boys is metal mesh but you can also use cloth or wicker baskets. These are a great place to store odds and ends like collection cards, baseballs, action figures, etc.
Homework Space
Try to incorporate a desk in your boys bedroom where he can quietly do his school work. A nice way to keep the area a calm space is to use a room divider. The divider can be done in such a way to incorporate the room's theme by either adding painted color, or pinning posters to it. A great idea on the desk side of the divider is to attach some cork and use it like a bulletin board.