How could anyone ask this question, "Who is the cutest little boy in anime?" and not name the most famous one of all, Conan Edogawa?!?
Detective Conan has only been in publication since 1994, and the anime is going on since 1996. He's the longest-lasting "cute little boy" in anime that I know of! (Okay, so what if he's really 17 years old? He still makes an adorable little boy.)
Next runner up for "cutest little boy in anime", but only because we don't get to see as much of him as we do someone like Conan, is Toushiro Hitsugaya, from Bleach! He hates being treated like a kid, but he still is only the equivalent to an 11 or 12 year old, so he counts!
These two cuties beat out all others IMHO.