Coraline > Paranorman > Boxtrolls > Kubo > Have not seen Missing Link but I'm admittedly not in a rush to do so.
Coraline gave me everything I wanted from a horror themed stop-motion picture. Strong atmosphere, creative visuals, fun distinct characters, a lovely soundtrack, etc. It's just a really solid blend of nightmares and childlike wonder.
I liked Paranorman a lot, but didn't think it felt quite as tight as Coraline. Half of the group was just there for hit-and-miss humor, and some characters, like the father and bully, were a bit too unlikable for their own good despite the film's message about acceptance. That said, I thought the whole climax was brilliant and genuinely emotional.
I can see why people give Boxtrolls flak for being the one to step away from horror themes for comedy, but I think when judged as its own thing its a fun ride. The villains are fun and over-the-top, and I enjoy the chemistry between Egg and Winnie, being two weird kids trying to understand each other's worlds. The trolls themselves aren't much to write home about though.
Kubo looks and sounds beautiful, and the choreography that they were able to pull off with stop-motion is astounding. But I think as a bigger adventure story it starts to suffer the most from awkward pacing after its really strong intro. I almost feel like it would have resonated with me better as a mini-series, going from set-piece to set-piece as opposed to one long disjointed field trip. Still good, just flawed.
Missing Link exists and it's an enigma to me.