#YOLOGNAISWAGETTI

As usual, I spent a lot of time thinking over this before I even considered making a decision.  The original list of candidates at the end of the year (after the initial series of in-brain eliminations) is as follows:
Tokyo Necro
Akeiro Kaikitan
Amatsutsumi
Karenai Sekai to Owaru Hana (knocked Inochi no Spare out of the running)
Tokyo Necro
Tokyo Necro is Nitroplus's first masterpiece outside of the Science series (Steins;Gate, for those who don't know what I'm talking about) since Muramasa, all those years ago.  As such, it is an obvious favorite, being the sole chuunige kamige of the year, as well as a solid story from beginning to end even without considering my personal tastes (if anything, the presence of zombies is a negative for me, normally).  It is brilliantly written from start to finish, with a masterful twisting of the elements of the setting to create a fascinating variance between the paths that made for some really interesting endgame story paths.  In addition, the characters themselves were awesome, acting out their roles within the story in a down and dirty way that you generally don't get in most non-rapegames.  In other words, this is Nitroplus at its dark and dirty best for the first time in over half a decade.
Akeiro Kaikitan
Like its predecessor, Nanairo Reincarnation, Akeiro is a brilliant blend of supernatural darkness with everyday life... and with real consequences rather than the moe goofiness that defines most such mixtures in VNs.  It has mystery, it has horror, it has catharsis, and it has great characters.  Depending on what path you choose, the protagonist's path through life is dramatically altered, as is the fate of the heroines.  This reminds me of why Nanairo won the incredibly competitive 2014 competition so easily, despite the presence of Bradyon Veda and a number of other awesome games.
Amatsutsumi
Amatsutsumit is a game for those who want a good cry, and it shows.  It lost out to Floral Flowlove in its VN of the Month competition, but the truth is that it should have been a dual winner, when it came down to it, since they were equal in quality from beginning to end, with only the ladder-style story structure causing me to rate it somewhat lower.  Seen apart from that, however, it is an ideal example of Purple Soft's evolution from a third-rate charage maker to a brilliant maker of fantasy nakige since the release of Mirai Nostalgia.
Karenai Sekai to Owaru Hana
This is 2016's biggest surprise, an overwhelmingly powerful nakige that doesn't bother doing much more than stabbing your heart with the plight of the characters and their travels from the depths of despair up the staircase of hope.  In terms of emotional impact, I can honestly say no other VN in this year even got close, which is why Inochi no Spare got knocked off the list by this one.  I'll be straight... I'm a sucker for the heroes drunk on their own heroism, and the protagonist in this one fills that bill perfectly.  As such, I literally spent hours in tears playing this game. 
VN of the Year Announcement
Those four were the final candidates when I moved to my inner-brain semi-finals, and they fought one another viciously for a place in the finals, then the golden Pocky of VN of the Year.  Karenai Sekai shattered Amatsutsumi in a battle that lasted only a few moments, and Tokyo Necro and Akeiro Kaikitan fought a brutal fistfight that ended with broken bones and Tokyo Necro's heel on Akeiro's head.
In the end, there came a brutal month-long battle in my back-brain between Tokyo Necro and Karenai Sekai, the two kamige blasting entire imaginary cities away in their attempts to claw out one another's guts.  Again and again, they shattered swords on one another's bones and regenerated from seemingly fatal wounds in an instant.  A continent sank beneath their feet, yet they continued to war with one another, even as their armies of followers drowned in the onrushing waters of the world's oceans.
In the end it was a matter of overall brilliance of design as a victory over pure emotionalism that resulted in Tokyo Necro being victor over Karenai Sekai, thus becoming VN of the Year 2016.  Unlike 2015, where there were few to choose from, 2016 was excellent, with numerous candidates from various genres to pick from.  While I won't go so far as to say the year was awe-inspiring, it was indeed a pleasure to read the VNs listed above, as well as those below.
Honorable Knockouts/Worthy of Memory
Floral Flowlove
Inochi no Spare
Senren Banka
Gin'iro, Haruka
Akiyume Kukuru
Ryuukishi Bloody Saga
Signalist Stars
Yomegami
Sora no Tsukurikata
Lamunation (this and Signalist were the best comedy VNs of the year)
Sakura no Mori Dreamers (knocked out of the running by Akeiro Kaikitan)
Soshite Hatsukoi ga Imouto ni Naru  (knocked out by Floral Flowlove and Amatsutsumi for nakige candidacy)
World Election
Koi Suru Otome to Shugo no Tate - Bara no Seibo - (sequel, so not a candidate)
Ou no Mimi ni wa Todokanai (two great games by AXL in one year...)