Ending
I'm not even going to try to answer all questions that my interpretation brings up but given all the talking about hindsight and how nothing is as it seems I think that there is more to the pretty obvious endings that have been discussed here before. My version might not be fully conclusive yet but maybe we can expand the theory and plug the holes together. This is what I have come up with so far:
[Beware of spoilers!]
I think the Cop is responsible for pretty much every death aside from the flashbacks.
First observation: What kind of name is Jeter? It sounds like cheater and it is just one s short of Jester which does not only perfectly suit the theme of card games as a card that fits everywhere and nowhere but looking at the cover art it also describes a darkly twisted character with plenty of tricks up his sleeve.
Some things about this whole kidnapping made it feel way too set up. I was nearly convinced this was all meticulously staged so Jeter would seem like the one and only killer once this was over. He was kept for days but always healthy though we never saw him eat or drink, the time lapses due to the drugging seemed a bit too convenient, the camera felt so carefully placed as to not reveal something we should guess for ourselves, during his escapes Jeter always was kind of enabled by the supposedly oh so clever killer, then there were the tattoo, the photos and videos and some more things I don't remember just now.
The way the lines are delivered so heavy with meaning and also as the whole thing turns out as a story in a story in a story probably told many times before from hindsight made me think that the words in this movie were very dliberately chosen. So when the killer talks about a new apprentice I was always expecting someone to show up or reveal himself as said apprentice. I didn't believe this just to be a decoy to lure the detective out of the house. Since I couldn't think of any character we got introduced to that would fit being young, influenceable and a bit crazy from the get-go better than her I really much thought the girl (Amy) would turn out as the apprentice when Jeter goes to get her before fleeing the house or maybe afterwards so she can make sure he is going to jail for the kidnapping. Since none of this happened but there was still no apprentice revealed (though one might say the clown at the end might have been the apprentice) I didn't get rid entirely of the suspicion I had before about Amy. Thinking about it we first see her beating what she says was a peeping Tom with a murderous look while talking to her police daddy on the phone - not exactly how one imagines a sane person. Since she is never shown again after her testimony which actually freed Jeter despite evidence against him I thought maybe that was the whole point and she is his apprentice after all making sure he, the killer, gets away.
(Amy doesn't probably need to be the apprentice. There might be no apprentice after all or the clown might work as well as long as Jeter makes No-Apprentice-Amy believe there has been a man with a mask.)
And that's when I figured there might haver never been another murderer with a mask. It was always Jeter's alter ego. Since we barely get to know anything about his past it might as well have been him who had some miserable years right after high school/college at a *beep* job, then killed his wife when she cheated on him and educated himself in murdering. What better way to do so by joining the police force. He got his mentor, filled the container with bodies and then got there on purpose and not so much by chance to kill him and get promoted. After that he feels bad about what he has done to his mentor (maybe even to his other victims) and develops a split personality. (Though the split personality might have existed earlier.) He then elaborately stages the whole kidnapping for himself to realize again who he really is and to convince/brainwash Amy (wearing the mask probably) into joining him. Come to think of it the man in the mask keeps repeating how Jeter and him are not so different after all.
Now come the tricky parts:
Firstly the torture. As we well know from Fight Club beating oneself up is not a real issue, but tattoing oneself might well be. What is that tattoo for anyway? Glueing oneself to a wall might be even easier then doing it to another person and handcuffing is also easily done without help. Taking into account that Jeter is insane and has to be making up some things to be convincing only to himself maybe we don't even get to see the real truth here. Drugging might just be fading out when the other personality takes control, the handcuffs might have been open all along or are maybe even just a symbol for being chained and not free and so on. This gets reinforced by the poker stories wherin Jeter embodies the part of the detectives faithful to the advice: "If you can't think it you can't see it and i you can't see it you can't learn." In addition during the first story at the poker night the audience learns that it can't trust what it sees when the guys are making fun of the narrator and we see how it would have played out in the flashback.
The interaction with Lieutenant Calabrese (Ron Perlman) and Maxwell (Titus Welliver) during the kidnapping is even more difficult to explain and i din't crack that yet, just some thoughts:
Right at the start of the poker game Maxwell (Amy's father) said something very dubios to Jeter along the lines of: "If I had a say you wouldn't be getting this promotion. You knew my rules you broke my rules. If this goes wrong I will *beep* you up." This could well be related to Jeter having an affair with Maxwell's daughter and Maxwell blaming him for her disappearance but it would also fit to Maxwell being Jeter's mentor which would make the guy who was shot at the container full of bodies just a scapegoat (Maybe rabbit guy?) to further Jeter's promotion which Maxwell is not ok with him.
Lieutenant Calabrese was the only one who didn't tell a story. He spends his screentime in flashbacks rescueing Jeter, interrogating him and telling him he has potential. Is it coincidence that Jeter is (maybe not genuinely) handcuffed the moment he realizes that the masked murder might be able to escape handcuffs?
But there are parts where someone representing the interests of the killer interacts with those two police officers and since they would have recognized Jeter it could not have been him. So the now unmasked murderer is right: too many lose ends, he would have needed help (Amy's actual abduction as shown to us included). My guess is that this is where clown and rabbit step in. Everything that can't be explained by Jeter suffering from split personality or slight delusions is done by clown/rabbit.
In the end Jeter sets clown up to take the blame for the murders which doesn't make the murderer smarter than Jeter but makes now smug looking Jeter smarter than any senior police officer he is sitting at the table with, since he is the murderer himself.
Granted, some minor and major details don't fit in there yet but a twist ending like that seem to much better strike the general tone the movie sets, don't you think?
Oh and btw, I don't really have an explanation in any scenario for the masked murderer making "sex with girls" his number one priority and yet we never really see him going for that. Though it is alluded to three times (Amy might be too old for him, he and his friends stop and speak to a girld, the last victim is a girl). Also what about that tattoo?