1. Little carries an emotional factor that small usually does not: a strange little creature, a little troublemaker.
2. It's a bit childish-sounding to say, "The house is little." Small often relates to physical size with objects/people - a small person/ a small present/gift.
Thus, the use of small when referring to a boy would reflect only his size and could be used whether the boy was 3 years old or 13. Little goes to age or maturity level and one might refer to an 8 year old (for example) as a 'little' boy even though he might be no shorter than average... or possibly even taller. Since young boys *are* generally of short stature, the two terms can often be used in reference to the same child.
3. Littlest is used primarily by preschool children, but by the age of 9 everybody says "smallest".