1. Saya no Uta
Urobutcher at his best (worst?). Featuring one of the most unique, chilling premises in any media and a gripping atmosphere, this VN never fails to hold your attention. The writing is concise, yet evocative, as it chronicles the protagonist's slow descent into surprisingly understandable madness. Professional and exuding excellence from tip to toe, it's no wonder that this VN is as popular as it is. I rate it my all-time favorite partly because of my preference for horror, but mostly because it's such a tight little black hole of concentrated awesome.
2. Umineko No Naku Koro Ni & Chiru
This work is special, not just as a VN, but as a literary work in its own right. The prose can be clunky and long-winded at times, but taken as a whole, Umineko a multifaceted piece working on multiple levels, each groundbreaking on its own right yet only working in conjunction with other levels. First of all, it is an immense, complicated ball of mysteries and riddles that readers can have fun solving. Who did not enjoy Bern's game in Episode 8? However, at the same time, it is a fascinating critique of the mystery genre and its limitations. It makes fun of the assumptions we rely on to make conclusions that we see as completely "logical", and reveals the empty base on which our thought processes are founded. The "red truth", with which we use to disprove the existence of witches, is only valid if we except the authority of the witches in the first place. On another level, it is a story that depends heavily on "nonsense and metaphor - but very important nonsense and metaphor", which is, I think a very risky and brave way of telling a story. It's a kind of subtlety that transcends realistic nuances - we have to actively work to decipher the narrative - any emotional investment we have in the characters and the plot seem to be very tenuous due to the nature of the story that blurs reality and fiction, mystery and fantasy, and yet somehow the emotions we feel ultimately make sense, if not on a rational level (ironic, that), but from a pure narrative perspective. The interaction and interplay between multiple levels of realities and fictions is astounding. And then of course you have the surface level of a family drama - all these interesting characters conflicting and colliding with each other. Lastly (and perhaps most important), Umineko works spectacularly as entertainment, especially in the Question Arcs where Beatrice is at the height of her trolling prowess. The exaggerated expressions and emotions of all the characters involved, the fantasy battles, everything - serves to exhilarate and leave you wanting more.
Being able to work on so many different levels and yet tie them together into one coherent piece of work is absolutely amazing. It breaks so many grounds on so many fronts while still remaining accessible and exciting both emotionally and intellectually at the same time. And how can you forget that amazing soundtrack? All those epic OPs and EDs? The heartbreaking BGMs and final song?
The only reason that Umineko is in second place is because unlike Saya no Uta, which is perfection from beginning to finish, Umineko does have some rough spots and weaknesses that drag it down. However, I think Umineko accomplishes more in terms of innovation and just the sheer scale and mindbreakingly beautiful complexity of its construction.
3. Animamundi
I'll be honest and say that this is here only because of my base desires: I love myself some hot gothic bishies and gory horror. And Animamundi is chock full of hot gothic bishies and gory horror. Of course, the well-written characters, complex story and well-paced conflict definitely helps as well. I just wis I didn't have to do so much backtracking to see all the paths. Definitely my favorite BL VN though. My other favorite, Enzai, has marginally better art (if not character design), but somewhat poorer story? If you can call the threads linking all the horrible prison rapes "story"? (Seriously though, this had some great stories and characters, but the potential never seemed fully developed - the sex was good, but I wanted the stories and characters to be a bit more well-developed). -sigh-
4. Ever17
Coco's route. 'Nuff said.
This game was a great experience. I cried at some of the endings. My heart was chilled. I was amused, frustrated, confused, amazed... and then Coco's route came along and my mind was blown. Such a great thriller. Of course, now that I look back on it, I can see how it might be somewhat overrated. Like Umineko, it does some really great things but is bogged down by some glaring flaws. The long-winded exposition, the "slice-of-life" scenes just weren't entertaining enough for me, and of course, the infamous kick-the-can. And even Coco's route has its problems. I highly respect it, however, for being one of the few visual novels that actually utilize the visual novel format to its maximum potential, like Umineko. You can't really adapt Ever17 to another medium without fucking up the story; that's how dependent the story is on the visual novel framework. And I think that's something that more visual novels need to do. Otherwise, why not just go write a novel, or publish a picture book, right? It's ranked under Animamundi, but only because I have a special soft spot in my heart for Animamundi and its delicious yaoi men - well, and how the prose can be really weak at times and the narration can be rather flawed at points and the ending relies on *cough* a certain deus ex machina... but again, same with the #1 and #2 picks, Ever17 does much more and is way more innovative and intelligent than Animamundi - too bad its flaws were so extensive it drove it down a rank.
5. Dangan Ronpa
The only reason it's so low on my list is that I'm following it through an LP, which has barely covered the second chapter - but I'm already loving the poo poo out of this game. It's like the Ace Attorney series in that it's mostly a visual novel with a bit more gameplay added on, so I'm counting it as a visual novel anyways. The story is incredibly addictive and exceptionally well-written, with none of the wordiness that so often plague even the best of VNs. The dialogue is sharp and exciting, due to all of the characters having ridiculously fun, over-the-top personalities - and I mean that in the best of ways. You can still empathize with the characters, and they're very well-drawn and three-dimensional (well, if you take good enough advantage of the social link-esque system), but the characterization and plot and art are all heavily stylized and the result is absolutely fascinating to watch. Have I mentioned this is a murder mystery? That it's described as Phoenix Wright meets Battle Royale featuring the voice of Doraemon as a monstrous teddy bear? It's great. You should either play it if you understand Japanese or
follow the LP if you don't. I haven't even played the game and it's already on my top five list.
Also, it features top tier seiyuu, for those for care about those things. (I mean, they even got the voice of DORAEMON. Who had retired and wasn't even planning to do anything after 25 years of voicing the same old blue cat robot. THE VOICE OF DORAEMON.)
Oh, and special mention because it's not really a VN but the gameplay is really VN-like: Rockett's New School <3
(I mean, I can't possibly type it all here, so if you wanna know more research for it 
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Why can't I find some japanese courses in this damn country?! 
