Scientists are still mapping out parts and functions of the Brain, but at this time they are fairly certain that memories are stored all over the brain tissue, with portions devoted to storage and reinforcement of specific memory types.
For example, the Hippocampus in each lobe of the brain helps create and sort short-term and long-term memory. The hippocampus takes important sensory input and translates it into a form that can be filed away and retrieved later, while keeping unimportant input "on the surface" where it can be forgotten without consequence. It works in tandem with the Amygdala, which sorts and stores emotions; the two memories are therefore connected so an emotion connects to a spacial memory and vice versa. Other parts of the brain sort pleasure/pain stimuli, and everything is stored across the brain tissue between neurons by connections called axons.