Intersperse short items with tall items. Even if your objects don’t necessarily carry a theme amongst themselves, you can still create a thoughtful, balanced presentation by concentrating on the size and height of items. Complement shorter, lighter items with taller, heavier items and vice-versa, varying their placement throughout the shelves.
Clear toy drawers are easy for little hands, as are lined baskets and open shelving. For larger items, utilize toy boxes, and also purge toys regularly as kids grow so you don't have more to organize than necessary.
Look at this idea book for other helpful toy organization: