Let's not forget this scene, where Dr. Sullivan hypnotizes Emily and she has a flashback where she kills Alison. She later says she got mixed up, but did she really?
Emily is the only of the four who had a real, emotional investment in Alison, who ends up breaking her heart.
They never explained why Emily blacks out and wakes up at Ali's memorial, only to find it trashed.
If Maya is, indeed "Uber A" (see below), then Emily would be the most likely accomplice, right? Just like Aria to Ezra.
Why It's Not Possible:
Emily's been severely drugged, and a car has literally driven into her living room.
When Maya gets murdered, Emily is devastated.
Emily seems to be the only one of the four Ali trusts.