Pandora Hearts ~ I know, I know, this was already mentioned but it's my most favorite manga ever ever ever and you can even see that in my review for the manga which I wrote like one or two years ago. But anyway—it's a must read. It's exactly what you're looking for and though it gets super confusing sometimes, it'll all make sense the deeper into the story you go. I influenced my friends to read this now we email each other after each new chapter comes out. Heck, I even got the pocketwatch! This is absolutely, positively, a series you must read. At all costs. It's also scanlated regularly so thumbs for that.

A Fairytale for the Demon Lord ~ great plot twists! A very great webcomic to read and it emphasizes much on fate and character development. Lots and lots of that going on. Did I mention it's full-colored? Well it is.

Kieli ~ one of my all time favorites. It's very unique, the plotline, in my opinion, and nicely executed. You get to see an interesting journey laced with religious politics here and there, no biggies, but for an atheist like me I loved it.

Goth ~ Okay, so not your typical guy story, but who says men don't enjoy a little twisted story-making involving a boy and a girl obsessed about murder? Huge twist there; it could be a double helix for all we know. Anyway, I'm not even sure if it's shounen but it's dark and twisted enough that guys should enjoy it too. It's more for the thoughtful reader though.

RustBlaster ~ some nice twists and turns but it's nothing compared to the author's later work, Kuroshitsuji. RustBlaster has some nice character development, mainly focused on the main character. Kuroshitsuji is great, don't get me wrong, but it's development is nothing compared to Pandora Hearts. Sure Ciel changes and so does Seb but it just seems so minor to me. Great read though!

________________
I am vindicated!
I am selfish;
I am wrong!
I am right,
I swear I'm right.
Swear I knew it all along
And I am flawed!
But I am cleaning up so well
I am seeing in me now
The things you swore
You saw yourself...

~"Vindicated" by Dashboard Confessional

Anything by Shirodaira Kyou, ergo Spiral, Vampire Juujikai (as someone previously mentioned), and Zetsuen no Tempest

Oh, and seconding the recommendation of anything by Urasawa Naoki, the manga Parasyte, Gunslinger Girl, Historie and Vinland Saga. And, in the scheme of historical mangas, I'm going to throw in Cesare, Shut Hell, and Shoukoku no Altair.

Also... Kekkaishi is also a fairly good shounen with (semi-)predictable yet interesting plot twists, Shin Angyo Onshi is a stunningly excellent manhwa, and Zettai Karen Children is an incredible shounen that has managed to stay consistently interesting for 300+ chapters.