Boxes
Boxes of all different shapes and sizes are perfect for stuffed animals. A toy chest at the foot of your child's bed is one type of box. If she prefers to have all of his or her plush toys where they can be easily seen, consider stackable square plastic or fabric boxes. These can be used as shelves on which to place stuffed animals. The ones your children use most often should be kept at a height level with their hands for easy access.
Nets
Nets allow your child to see all of his playthings, but still keeps them off the ground. Hang netting above his bed, for instance, and simply place the stuffed animals inside. The advantage of this method is that if you purchase netting with an elastic quality, you can fit more toys into it than you would think. A word of caution, however: do not use netting with small children, or they may try to eat or get tangled up in it.
Clothing Organizers
Clothing organizers -- the kind you see for shoes, sweaters, and belts and ties -- can be used to store stuffed animals as well, and place them in the closet so the bedroom stays tidy. Use larger ones for the larger toys, and place any with clips or hooks on them on hangers used for storing belts, ties and scarves.
Considerations
Sometimes, no matter how you try to organize stuffed animals, you simply have too many for your child. Get rid of ones that he has outgrown, or with which he no longer plays. These can be donated to charity, or, if they're too worn out, simply thrown away. Try to get your child to be a part of this process so that he doesn't feel put out when items are discarded. Let him make decisions about what to keep and what to get rid of -- as long as every item doesn't go in the "keep" pile.