Silent Hill 2 ending.
Silent Hill: Shattered Memories ending.
Xenoblade X ending.
Corpse Party ending.
Fatal Frame IV Choushiro Kirishima ending.
Spirit Camera final boss twist.
No One Lives Forever (each plot-twist in this game is hilarious).
Resident Evil Remake (Lisa Trevor ending).
Everything about To the Moon plot.
Wonderful 101 pre-ending twist.
Resident Evil Darkside Chronicles (Manuela Hidalgo twist).

Yeah I just cannot remember that being topped in recent times honestly.

Borderlands 2.  First, the death of Bloodwing was just brutal and then the death of Roland while everyone was pumped up about your victory.  I thought both were very well done.  The second one, especially, surprised the heck out of me.  

Final Fantasy VI.  When the ending turned out to be just the half-way point, with Kefka turning on the Emperor and destroying the world.  I thought that was bloody awesome when I was a kid.

Final Fantasy Tactics.  Just everything.  The whole thing was a story of twists.

For story I would say Professor Layton and the lost future. If you played the game, you would know what I was talking about!

Not sure for gameplay though.

Xenoblade X had a few great twists. The epilogue though, that's the best twist I've experienced in a while.