I can think of three reasons that the name Emily may have been chosen for the title of William Faulkner's short story. First, Emily has always been a popular name in Western culture, so the author may have wanted to show that she was of common heritage. On the other hand, the name "Emily" is derived from the old Latin/Roman names Aemilia and aemulus. In Latin, aemulus is defined as "rival," a distinction that Faulkner may have wanted to illustrate. Aemilia (or Aimilia) was one of the most important families in ancient Rome, and many of its members held high positions for centuries. Faulkner may have chosen this name to symbolize the former power of Emily's own family name, the Griersons. Additionally, as the other post mentioned, Faulkner may also have sought a comparison to poet Emily Dickinson who, like Emily Grierson, lived a sheltered life (rarely leaving her home) under a domineering father before dying a maiden spinster with no children to carry on the name.
I don't know about you, but when I hear the name Emily, I picture a cute, petite blonde, young and innocent, cheeks rosy and always wearing a smile. Emily is the name of the perfect daughter, a sweet wife, an innocent, though it has an element of strength (Emily Bronte and Dickinson, case and point). The name Emily then becomes a perfect means for the writer to make the ending all that horrific. Not all is as it seems, the girl is not just a girl, nor is she innocent. The title itself forces you to unwillingly draw conclusions about what the story will ultimately be about, and because the ending is so drastically different from what you immediately perceived, then you have an even greater shock at what they end up finding in her house.