First, my evidence. Of course, this is all just from reading - the documentary sways towards their innocence and other people sway you towards their guilt. There's really no concrete answer here, the only people that know are those 3 boys that were killed and the WM3, or whoever truly killed them.
1. Jessie repeatedly confessed to the killings. He confessed after a couple hours of being interrogated, failed a polygraph, and confessed to his lawyer a week later. He confessed to friends, he wrote statements confirming his guilt, confessed to cops transporting him to prison, confessed to prosecutors, confessed to cell mates, and supposedly confessed to counselors in prison. The documentary would have you believe he was coerced into confessing after several long hours, but that wasn't really the case according to documents:
Jessie Misskelley June 3, 1993
That link has a timeline.
2. Physical evidence: The lake knife - a knife found in a pond in Jason's back yard. It had a compass missing from the handle, and experts have claimed that this matches the "bite mark" wound on Stevie's forehead.
Damien's bloody necklace - Damien had a necklace that had both his blood and the blood of two of the victims on it. It was never presented in the trial because it was discovered late. Apparently it is not able to be retested as the blood samples are depleted.
Knots - all 3 victims were tied with 3 separate, different knots. This is only coincidental, but leads one to believe that this is the sign that 3 separate people participated.
Blood - the documentaries say there was no blood on the crime scene, however investigators have said that luminol testing at the scene showed large amounts of blood. This confirms Jessie's confession of where the murder took place.
People saw Damien walking near the crime scene with someone and was covered in mud around the time of the crime, those statements were never recanted.
3. Alibis: Echols said he was on the phone with a few people during the time of the murder. All 4 of them claim they didn't talk to him during the time of the murder but one person in particular, Jennifer Bearden, talked to two of the WM3 before the murder and was told to call back at 8PM. She called back at 8PM and Damien still wasn't home, she couldn't talk to him until 9:20PM. Additionally Damien told her that he had been out with Jason's mother, but Jason's mother had already previously stated she was at work.
4. Softball girls - Damien was bragging on a softball field to some girls about killing the kids. The documentaries claimed at least one of them recanted, however none of them have. Damien even admitted he did that, as a joke he claims.
There's a slew more of stuff, but I picked out the stuff that interested me the most. I used this place as a source;
West Memphis Three Facts - Home
I couldn't remember all the details so I picked up the stuff from the website that I remember catching my eye years ago. Obviously the website is a bit biased and over the top.