I'd say Your Lie in April qualifies. Yes, they telegraph the ending from very early on. You know it's gonna happen. They swerve a couple times. You think maybe it won't. Then it does. "Ah, that sucks, but I called it from the very beginning," you say. Then the story keeps going, and just when you think "oh yeah what's with the title? It never made any sense," they explain the title.
Angel Beats! is another good one. It's about a purgatory school. They tell you the girl called "Angel" is trying to get people to move on. She kind of is, and eventually those opposing her realise that's the right move, but there's a lot more to it than that. Ask yourself why she's trying to help others when everyone else is just out for themselves.
Then there's Sword Art Online II (the second season). The first part, with the gun game, kind of has a twist — how a guy in a video game that should be harmless is killing people IRL by shooting them in a video game. It's pretty lame, though. The second part, the last seven episodes, if it were a standalone anime, it would be my favourite anime. The adaptation of book 7, Mother's Rosary. The secret behind the undefeated duelist.