Considering everything that everyone collectively knows (excluding the police), there aren't a lot of answers out there. It hasn't stopped people from formulating their own pet theories. Some of them have been quite bizarre. This webpage runs down most of the theories I've heard over the last 10+ years since the murders
This theory proposes that Neal and Brendan were murdered because of some kind of involvement with illicit drugs. The theory arises because they were murdered "execution-style," a mode of murder firmly associated with drug wars and the gangs that push drugs. Now as far as anyone can tell, the murder style is the only reason to connect the Abernathies with a drug-related murder. Otherwise, the thought of the Abernathies being involved in drugs is beyond laughable.
There's a varient of this theory that holds water much better. The varient maintains that the murderers visited the wrong house and that Neal's and Brendan's death was a really tragic mistake. It has the virtue of being plausible, unlike the "direct involvement in drugs" theory. Again, the only known evidence supporting this theory is the style of the murder. Tying the murders to drugs, however, merely on the basis of the murder style is actually pretty weak: while many drug-related murders are execution style, not all execution style murders are because of drugs.
Thrill murders, like serial murders, are the most difficult to come to terms with becuase there is no real motive other than personal gratification and the whim of the murderer. Could Neal and Brendan be the unfortunate target of such a crime? Again it is plausible but evidence is quite thin on the ground here. Many crimes in the thrill/serial category only come to light when a killer confesses.
This flavor of theory has one big problem with it: very little was actually taken from the house and the police stated that the meager signs of burglary could have been staged. That last bit suggests that the murderer or murderers wanted to obscure their real motive and introduce confusion into the crime scene. I think this theory doesn't hold water.
This theory is an obvious one. Neal owned a business. Neal went through several managers and a lot of staff over the 6 or 7 years that he had his garage. It is certainly plausible that someone Neal let go went postal on him. It would certainly explain the mysterious note and phone call, two circumstances that do not fit burglary or drug-related scenarios.
The varient of this theory is that the murder was committed by a disgruntled customer or ticked-off neighbor. Going postal is not reserved to former employees. There's a twist to the disgruntled employee or associate scenario: whoever murdered Neal knew he was home that day. So who knew in advance that Neal was taking time off to spend time with Brendan? Now the burglary scenario doesn't require foreknowledge of Neal being home nor does the thrill murder scenario. All the rest of the scenarios require some kind of knowledge that Neal was at home that day.
This scenario already has a suspect built-in. Neal and Brendan are murdered to get them out of the way. The murderer then moves in on Susan and marries her on the rebound. This would make Susan's second husband the murderer of her first husband and son. There's motive, means and opportunity! It's an obvious theory to chase - except for the lack of evidence... This is one theory that should be easy to resolve given modern polymerase DNA methods - and we know that DNA was looked at by the new California crime lab. It doesn't explain the note or phone call either.
There's no way around it: we can not escape the allegation that Neal was mudered because of the Promis affair. It already has its own webpage in this website so I won't repeat the details here. I will mention one thing, however, related to the Promis nonsense. Every now and then, I'll be contacted by another journalist sniffing around the Promis story. One of those journalists once told me that he had heard that Susan Abernathy had a romantic interest she had met sometime in her youth through connections in Canada, and that this nameless person had connections to the national security council. Somehow because of the Promis link, this nameless person used his ties with the national security council to get Neal bumped off. I pointed out that Susan grew up in solidly middle class circumstances down in the LA area, which is not exactly the right venue for making connections in Canada and with nameless national security council members. Really, some of this conspiracy theory crap is way out there.
Susan came home and found the door ajar. There were no signs of forced entry. This has been remarked upon by any number of Neal's friends as evidence that Neal knew his killer. The murderer got into the house without a struggle. It's not good evidence if you think for a moment. The killer knocks on the door. Neal or Brendan answers it. They open the door to see who is there. The killer or killers stick their gun in Neal and/or Brendan's face and walk on in as Neal and/or Brendan are forced to back up. The door is opened and the killer or killers enter without physical evidence at the door itself. Forced entry does not have to involve damage to the egress into the house. The Abernathy house was in a good neighborhood, one where street level crime doesn't really happen. Opening the door to a stranger is not beyond the realm of plausibility. Finding the door open is not clue that will explain this murder.
The fact that the Richmond cops sent DNA evidence for renewed testing at the new crime lab in Richmond means that there was at least some physical evidence that could tie the killer or killers to the crime scene. The fact that they haven't developed something by now suggests to me that the killer or killers were careful enough not to leave a lot of evidence behind - or the cops would have developed it by now. Or maybe they already have but don't have enough to convince a jury. Without knowledge of the evidence gathered to date, it is difficult to second guess where things stand on solving this murder.