By means near, beside, or past. When your friend rides by on her bike, she passes close to you.
Your dog might run by too fast for you to catch her and put her leash on, or you might ask your dad to drive by the house he lived in when he first met your mom. In both cases, by means "past," or "passing a particular point." A more old-fashioned way to use the word is to mean "aside" or "in reserve," as when your aunt puts some homemade pickles by so she can eat them all winter.