In 2x14 when the girls are in orange jumpers cleaning up garbage, Emily and Spencer start fighting.
Spencer says "you can't make a deal with a rattlesnake", Emily responds "you can if you have something the rattlesnake wants"
Then in 3x11 Spencer is attacked by a rattlesnake in a change room.

in 4x08 when Emily was talking to Ezra in the classroom as she is leaving Ezra says to her "Somebody's gotta remind you who you really are Emily"

In 4x08 Emily is talking to her old councilor and her councilor is saying how good she was at drilling but then at the end of the same episode in the A scene...A is seen drilling holes in something.

3x01 Aria is in a bathroom stall and thinks she sees A through the crack after she can't get it locked. She begins to freak out and eventually Spencer and Hanna show up. But where was Emily?

We have seen a red coat hanging from Emily's closest door. (see pic)

At the very start of 4x01 when all of Mona's files get deleted and they hear a little kid from outside say something. if you listen cloesly he says "She's not there Aria, it was Emily's idea", hmmmm.

In 2x02 Emily gets scouted and a business card from a rep. at Danby. There is a note she gets (supposedly) from them that reads "So Happy to Have You on Our A-Team". Could this have a double or alternate meaning? Plus we see a paper in A's lair with the same Danby notepaper. (see pic)

There is a time walking to school that Emily says to Hanna "Maybe I'm not the person everyone thinks I am"

When Dr. Sullivan hypnotizes Emily, why does she have the memory of her with Ali on 'that night' and she is holding the shovel and wakes up as shes about to hit Ali?

How was Emily the only one drugged when all the girls were drinking from the same flask?
But why would she drug herself? Let's go to the 3A finale When they thought Paige was A...
Spencer said that Paige drugging herself was a classic Sharon Stone move. This is a reference to a movie where a woman wrote a murder mystery novel to cover up for the murder she was about to commit.
Could this be what Emily did?

Also about Emily being drugged (this comes from 3x08), Paige says to her "If I ever find out who put that stuff in your flask, I swear I ll kill them"
and Emily gets very mad at this saying "I don't want you to say that and I don't want you to mean that"
Could this be because it was herself that did it?

Emily seems to come away unharmed from any event that should harm her. The barn and the woodcutter are examples of this.

Emily wrote a letter to Alison three days before Alison's disappearance.
A line in the letterse reads "You're not afraid of hurting me, so I wonder why I'm so afraid of hurting you". Suspicious?

This may not be anything but it's worth saying, when Emily is talking with Dr. Sullivan after Nate's death she says,
I killed someone. Someone had a life. Someone was a living, breathing person. We assume she's talking about Nate, but maybe she's talking about someone else (like Ali) or others

The episode after Ezra tells Aria about his book, at the start the 4 girls are in a room together and Aria says "He thinks that one of us did it" and Emily immediately says "Well now we know it's a work of fiction"

In a Hollywood Life interview Brant Daugherty said he thinks Emily is A.

And the biggest hint of all I think is... "A" watches wheel of fortune and Emily has said "I've been watching Wheel of Fortune with my mom since I was 3"