Hey there swtrooper42 Just came by to thank you for suggesting Swan Song (going to finish the rest of the suggestions in time) but I just had to say... wow when I play this visual novel, each individual character with their own problem and how things go in a realistic manner towards a disaster. How well the story contracts the emotions of religious people/cruel people, and especially with the one scene where you are begged to kill Aroe to release her from the misery of this world. I'm just in awe, thank you again for the suggestion.
Here are some detective, mysterious VNs with a somewhat dark setting depending on how you view it. G-Senjou no Maou ,Sharin no Kuni
These two fit perfectly, they are extremely heavy-story-based VNs that just make each and every heroine lovable in their own unique way (although if you had your eyes set on one specific heroin, you will have to go through the other heroine's chapters first to get to her) Koihime Musou
This VN is if you are into the Romance of the Three Kingdoms story but all those generals in that era are females! So many heroines to acquire your mind will explode! The gameplay of this VN is somewhat non-challenging and very easy to blitz through so you can imply that they just wanted you to go through the heroines Symphonic Rain
Since you are playing Little Busters, that implys that you don't only play 18+ games so you might want to check out Symphonic Rain, a story with a setting about the male character finding a partner for a musical contest or else things will never turn out right. Especially in a city where it rains 24/7. This VN primarily focuses on you playing the piano (mini-game) and requires you to focus on the soundtrack in those specific games... (sadly there is no music outside of the mini-games)
Cross X Channel
Yume Miru Kusuri (A Drug That Makes You Dream)
There might be some that I'm missing but that's all I can remember for now. I would prefer them English translated.
My top 5 would be Fate/Stay Night, Cross X Channel, Clannad, Family Project, and Little Busters.
I also recommend Family Project. A truly moving VN that easily places in my top 3.
It's about a bunch of social outcasts who for various reasons come to live together as a "family" and learn to depend and trust on one another. Although it can be rather sad and melancholy at times, it's rather cheerful.
It's also written by Tanaka Romeo, who wrote CrossXChannel and A Drug That Makes You Dream.