We use the ikea expedit shelves. They have cube shaped holes with fabric drawers perfect for toys. For our larger collections such as Thomas train set, duplo, dolls, dress-ups we have plastic wheely bins ( not sure if this is what you call them in the US, perhaps trash bins on wheels). I also have various bookshelves where other toys, games, farm house etc are stored. When all my kids were small, I had a melamine pantry cupboard with a small padlock and chain around the handles. I let out small tubs at a time and kept the rest locked up.
