'Made of' means that the object is made entirely of this material, and that the material is unchanged. For example, 'These shoes are made of leather' or 'This bottle is made of plastic'. The leather that the shoes are made of is still leather - it has not been changed into another substance during the process of making the shoes. 'Made out of' has a similar meaning, but the implication may be that there is more work involved, or that this is an unusual use for this material, for example, 'During the famine, people made shoes out of straw and rags.' 'Made from' means that a raw material has been transformed into something else. For example, 'Cheese is made from milk'. You don't usually say 'Cheese is made of milk', because the milk no longer exists - it has been transformed into another substance. Likewise, 'Glass is made from sand'. Sand is the raw material, but it has become something else in the process of making glass. I hope that makes sense.

Both of the answers previously given are excellent. I thought I'd just add that you can also use, 'made with' to mean, 'partially but not entirely made of.'

At first glance, and even after a little thought, all of these mean the same thing and can be used interchangeably. "Made from" is the most technically correct. If you're writing, use this one. "Made out of" is still rather technically correct. You can use this one in your writing as well, but sparingly. If you use it over and over, it'll look a bit strange. "Made of" is often heard in everyday speech, but is not technically grammatically correct. Feel free to use this in conversation, but it will be noticed as informal in writing. As I said, they all mean precisely the same thing.