how many actually stories are happening in this anime. Is it all one? If so, I don't get how all of them relate.

Those are all different stories. What happens is that in every story there's a "bad end", where some of the characters get killed, or where everyone dies in Hinamizawa (I hope I spelled that correctly). When that happens, everything restarts and something changes, leading to other events. Oyashiro-sama, or whatever the name of the god Rika can channel, seems to be responsible for this. So basically, everyone's stuck in a giant time loop until a "good end" occurs. What's unusual in the last arc is that Keichi manages to remember stuff that happened previously in a different timeline. Usually only Rika could do that. The last arc appears to end with a "good end", but we see that there is another restart anyway. Rika/Oyashiro-sama even mentions that there is another mystery in Hinamizawa. This is because, even though we do not see it, everything ends badly again. To be more specific, everyone in Hinamizawa dies just like in one of the previous arcs. The reasons for this is the other mystery Rika refered to.

Of course, this assumes I've managed to piece the whole thing together correctly.

How in the blue hell can they talk about some mystery, and never even give us any clues on what it is? This kind of ending leaves me REALLY sour after such a good anime. Seriously, i'm pissed off...

Keiichi shot little girls with a toy gun, he never killed any of them :p

I'm still kinda surprised that there wasn't an elaborate double-jeopordy trap in place in/around the building. I mean, when Shion (episodes back) promised not to kill Keiichi, it looked like she held to that promise...until the end of that episode, of course.

shoot one of those girls in the eye, though.

I hate Shion in the second Mion/Shion arc. Needed a more satisfying death.

Last Arc is the best... but really sucks that it doesn't conclude EVERYTHING. So those of you who know the games... who's really behind the shit that went down and why?

I haven't played the game, so I can't explain the whole thing. What I do know is that there are apparently 3 things going on in the village. First, there's the stuff tied to Oyashiro-sama, namely the restarts and Rika being able to predict some things, which I believe I've explained in a previous post. Next, there apparently is something known as "Hinamizawa Disease", which is responsible for all the crazies we get to see (Keichi, Shion, Rena). I'm really not sure about that though, since I haven't heard much about it.

And then of course, you have the one who triggers everything each time. That would be Takano. Major Takano, actually. It appears that she is an officer in the JSDF, Tomitake also being one, though of lower rank. In each arc, she has a disagreement with Tomitake, and ends up killing him then faking her own death. The guys we see going around in vans are apparently with her. She also seems to be responsible for the "Hinamizawa Disaster", where she gasses the whole town. The reason of her presence is apparently related to the Hinamizawa Disease, in fact, I think I remember reading that Dr. Irie is part of the research on this. I'd really like to go into more details about this, but unfortunately, I don't know much more and I don't have much time either.

And for those wondering, the deaths on the previous Watanagashi (or however you spell that) nights were actually coincidences. I think.

-Oyashiro-sama is actually a cute girl spirit with horns by the name of Hanyuu. Her powers only include resetting the world when Rika dies, but her powers have dwindled. Those infected with the Hinamizawa syndrome could hear Hanyuu, but only Rika could see (and in the anme, 'channel') her.
-Takano's motivation? Simple but two fold. a) To become remembered like a god b) Continue her grandfather's research and avenge him... it's believed the town disgraced him, thusly she gasses the town out of revenge in some endings
-In the seventh and eighth arcs, Rika slowly comes to know of Takano's motivations. As well, the other kids stick their friendship together to make sure nothing goes wrong... But that's when Takano leads an assault and kills them all (seventh arc)
-Last arc apparently has Rika know of Takano's motivations right from the start. A few miracles later and arc eight plays out like seven--minus the good guy deaths. By some last miracle... the one I'm hunting for to this day, Rika kills Takano.
-As well, Takano is fleshed out, and apparently is in tears by the time Rika finishes her off. Ouch.
-I would like to mention again that I still have no summary for arc eight and therefore have no idea what miracles occur to allow Rika to achieve victory. Which makes me quite angry actually.

How it starts off so gruesome, but then turns into something lighthearted in episode one. Then it turns into something horrific at the end with the discovery of the whole dismemberment murder that occurred in the past. The juxtaposition between something light-hearted and something so much more horrific is just crazy to me - and I love it.