Deputy Sacks was the real power behind the Neptune Sheriff's Department
At least when Lamb was in charge. It seems like Sacks always did all the work and all Lamb ever did was public relations. I recall a scene or two where other deputies would come to Sacks with information or for orders instead of going to Lamb.
Aaron didn't kill Lilly/Logan did and Aaron took the fall to protect his son
Logan killed Lilly, having been driven to madness by her blatant infidelity. Aaron eventually figures this out when Logan is arrested and due to a variety of factors (guilt for driving Logan's mom to suicide/physically abusing him to the point that Logan was incapable of remembering the good moments of his life, only the parts where his father beats him mercilessly/fear of having passed down his own abusive father's genes down to his son), springs into motion a plan to take the fall for the crimes. Logan never finds out until after the fact, when Aaron tries to kill Veronica/Keith and manages to convince both that he was the killer. Logan becomes guilt-stricken as a result (being framed for murder doesn't help) and he basically breaks up with Veronica because of this, as he Logan begins to self-destruct and with Veronica getting on his case for letting Dick and Cassidy convince him to torch the public pool, Logan dumps her rather than risk confessing to the woman he loves that he murdered Lilly. It's also why he bought and destroyed the sex tapes of Aaron and Lilly from Leo, in order to try and save his father and why Aaron's lawyer didn't cross examine him (Aaron didn't want to risk Logan breaking down on the stand, especially since he had his own scheme in place to ensure he was acquitted). It would also explain why Aaron attempted to reconcile with him after being acquitted/why Logan didn't violently lash out at him after the trial (Logan knew his father was innocent) and why he was so willing to confess to Veronica in the elevator: to ensure that Veronica would forever think he was the killer by way of outright admitting to it.
Aaron killed Lynn
She was destroying his image, and he has a violent temper. We see him stand after she storms out of the school in "Clash of the Tritons". He faked the note and threw her off the bridge. His reaction in "Lord of the Bling" was a My God, What Have I Done? moment.
- Rob Thomas has stated that he made Lynn's death ambiguous in order to leave the door open for her possible return.
Cassidy was in love with Lilly
Everyone loved Lilly. Everyone.
Besides, if he's really that insane and has such disregard for human life, then why would he feel compelled to report Logan's false alibi? Either he places a higher value on Lilly's life than others', or he did it because he wished to punish Logan. This covers both those reasons. Her death likely was the Despair Event Horizon for the damaged teen, leading him to... well... become what he was.
Cassidy told Veronica about Logan's false alibi in Tiajuana because he was jealous of her being in a healthy relationship.
Cassidy never believed Logan killed Lilly. This reveal came one episode after Cassidy had seen Veronica going all over school investigating her rape, obviously still angry and hurt when she confronts him. At the end of "A Trip to the Dentist," Cassidy sees Veronica and Logan happily making out. Then in the next episode he's ruining her relationship by telling her something "for her own good." We know Cassidy couldn't have a healthy sexual relationship with Mac the next season. Cassidy (not knowing about what she had found out from Duncan) was jealous of Veronica's ability to get over her rape when he hadn't been able to. Alternately...
Cassidy told Veronica about Logan's false alibi in Tiajuana because he genuinely wanted to protect her from possibly being murdered.
Cassidy believed Logan was responsible for Lilly's murder. Cassidy felt guilty for raping Veronica and was trying to make amends by keeping her safe from her murderer boyfriend.
Lilly Kane was Weevil's little sister
Irony and Squick in this "Lilly's my sister's name" thing from Girl Next Door. Hey, Weevil's mom could have been a maid in the Kane household, and so it's possible.
It's also a possible explanation for why she ended it so abruptly and went straight back to Logan.
Weevil never knew.
- Really only workable if Weevil's dad knocked up Celeste, since the Kanes wouldn't accept a child of Jake's otherwise, as seen with Veronica.
- It's perfectly possible that Jake slept with Weevil's mother and so he's Weevil's father in addition to being Duncan and Lilly's. That covers them being half-siblings and why, if anyone knew, Weevil was never taken in.
After leaving Neptune, Veronica moves to New York, where she puts her investigative skills to work as Gossip Girl.
Kristen Bell plays both. Veronica Mars IS Gossip Girl.
OR Veronica goes to work for Abstergo
After getting a Biology degree from Hearst (specializing in genetics), she finds out that the Mars' are connected with the Assassins, she changes her name to Lucy Stillman. She continues in school, eventually getting kicked out for her radical ideas in genetic memory, when she is suddenly apprenticed to Warren Vidic at Abstergo.
Thumper didn't kill Felix
Weevil figured out it was he because he was connected to the Fitzpatricks - but when Weevil confronted everyone, they all seemed on Thumper's side and not at all shocked about the news. They were all more or less in line with the Fitzpatricks by then.
Thumper had nothing to do with Felix's death. He got out of there before it happened and thought Logan had done it.
So who did kill Felix? Perhaps it was long-dead Cervando, but we don't know his motive.
Troy Vandegraff was interested in Veronica because he had heard and believed the gossip about her promiscuity.
I don't know that this guess is all that wild, but it would explain some of Troy's behavior. He doesn't plan to stay in Neptune very long before he runs off with his old girlfriend in the car he stole from his father and the proceeds from the drugs he stole from Luke, but he figures he might as well try to get laid while he's waiting. And here's this pretty girl whom everyone is telling him is easy. Why shouldn't he believe them? Of course, all the people who were around before and knew Veronica know that the rumors aren't true, they just repeat them to hurt her.
Lianne Mars is Lilly's mom.
Another theory my boyfriend came up (early on, before it's revealed that Jake Kane might be Veronica's father) was that Lianne Mars is Lilly's mom, and that that's why Celeste was so much harsher to her than to Duncan. It would make sense, maybe she was born before Lianne was with Keith, and then things got blurry with Veronica and Keith wanted to keep her.
Veronica Mars is schizophrenic.
Think about it: in "Kanes and Abel's," she, while fully awake and aware, sees and has an extended conversation with the long-dead Lilly Kane. Seeing things and hearing voices is practically the definition of schizophrenia. And she has at least some of the symptoms of paranoia. Plus, she is in her late teens; that is generally the earliest schizophrenia manifests. Also, consider that schizophrenia can often be an inherited condition, and that her mother was an alcoholic. Maybe Lianne Mars was self-medicating for her own symptoms. Lastly, consider what Aaron Echolls says in the season one finale when he has Veronica trapped in the fridge: he goes on this whole rant about Joan of Arc and how the voices she heard were really symptoms of schizophrenia. Why would that occur to him? What if Veronica is a highly organized, high-functioning schizophrenic?