Lot's going on here...

You've got themes like how pedophile victims (men especially) are ostracized because it is known that victims are more likely to become them themselves, then ironically losing their life because they live in this void where they can't really talk about it, but also have severe mental hang-ups about it.

You've got themes where women having far too much influence on the men in their lives because they seem like they are intelligent yet innocent, but one of those hats has to drop. - Boyle's wife thinks he murdered Katie even though he really is just afraid of getting caught for murdering the other guy - Jimmy's wife is so protective of her brood that she prevents Dave's kid from ever knowing the truth about his father being murdered through a mistake - Yeah, like that isn't going to come back and bite that family repeatedly til the end of time.

You've got a coerced confession from Dave to Jimmy because then he'll live.

You've got the real motive for killing Katie very likely being innocent (swerved to miss the kid in the road, accidentally shot.) Yet, that situation causes numerous acts of violence: The death of Katie, Death of Dave, Beating up the kids by the older brother.

You've got an open ending so that the viewer can decide what's going to happen, but we really don't know.

What stands out to me most though is the foreshadowing of Dave at the beginning when he knocks the ball puck into the sewer drain:

Dave: I guess I don't know my own strength.
Then years later Dave accidentally kills a pedophile with his bare hands and is rocked by this and has to hide the body and lie about it to everyone while his friend's daughter just died.

I think after all the senselessness of the whole thing I like to think that Jimmy and the cop just drop the whole thing because it really is messed up situation for those two murders to happen on the same night and Dave just handled the situation poorly, innocently on some level, maybe, because his hang-ups about his victimization, but just very very poorly.

In the end, makes a good movie that's hard to predict what's going to happen, though, with a ton of suspense built up with very good acting from Penn in the scene on the porch with Dave.