EXPLANATIONS
Melissa and/or Spencer's Dad: The Hastings are well known for being perfectionists (example: Spencer's mother never telling anyone in the family about her possible breast cancer in Season 1/Melissa not telling her her family about loosing her child). As explained in Season 2, Jason is Spencer's father's son. Knowing Alison's sneakiness, Alison probably knew of this and wanted to expose the Hasting family. Spencer's father probably killed her with the "blunt instrument" (field hockey stick which he burned in Season 2) to keep her from exposing them. Melissa could have also killed Alison because she was seen on the video with her and Ian speaking of Alison moments before she died.
Byron: Alison and Aria caught Byron with Meredith. He could of possibly killed Alison to keep her from telling Aria's mother (remember: she repeatedly told Aria to tell her mother and eventually "told" her herself). Byron, then, left the country for a year so that no one could suspect him.
Aria, Spencer, Emily, and/or Hanna: It'll be an unexpected twist (I think it'd most likely be Spencer) but there may be a chance. Alison (yet again) could expose their secrets (Hanna's bulimia, Emily being gay, Aria's father, and Spencer with Ian). If you've read the books in which they'd show flashbacks of the girls with Alison, you would know that Alison constantly taunted the girls with their secrets. EX: In Perfect Emily says to Alison "I'll do your hair you have gorgeous hair cherie." Ali replies "Doesn't cherie mean girlfriend?"
Spencer in Particular: Spencer and Ali always clashed in the books. At one point, Spencer pushes Ali to the ground, harshly after hearing a low blow. This shows Spencer's short fuse. In both the show and book, it's Spencer who kicks Ali out of her sleepover. When the girls wake up to find out that Ali is gone, Spencer emerges into her farmhouse and tells them that Ali is gone. She either have witnessed Ali being killed from her father/Melissa or killed her herself.

I HIGHLY recommend the books (as you can see) xD

I love the books they are so good. I can see all of these being a possibility.

I don't want the show to be like the books: I never liked the twin theory!

^the show and the books are on two completely different wavelengths. The show followed only the first book (first couple episodes) and a tiny portion of the fourth book (finding out that "A" was Mona). Then went off on its own.

I really believe it's someone we haven't met yet.

I don't know I don't know everybody could have killed her, everyone is a suspect for me...

I honestly have no idea I think that everyone is a possible suspect (after all Ali did piss off a lot of people) so anyone of these people could have done it) although I don't think that it was Hanna, Spencer, Emily or Aria I'll admit it would be a huge twist but I don't think that any of them would really kill Ali. Oh and I also don't think that Byron did it again it would be a huge twist but I don't think that he would have killed Ali just to keep it a secret Ali was one of Aria's best friends and I just don't think he would have it in him and anyway Ali isn't the only one who saw them together Aria did too I know he probably wouldn't kill his child but I still just don't think that he has it in him.

I guess