Lucid9 is one of the best free visual novels I've ever played.
It's about a guy that goes to a prestigious boarding school that, of late, has had several students go missing and later show up murdered. But the story as a whole's not 100% dark, and there're some lighter hearted slice-of-life moments as well. The climax near the end is also my single favorite individual scene in all of fiction.
What's out right now is the "common route" that will be followed by individual "heroine routes" (The first of which is nearing completion) and later a "true route."
There are choices to decide which of these routes you get, but it's possible to fulfill the requirements for all of them and then choose one at the very end. I'd even say it's fairly easy to do that, as I was able to do it without a guide despite choosing to see all the joke "Gover Mecher" sequences. Just save at every choice in case you need to go back and you'll be fine.
Anyways,
Project Kat and it's sequel
Paper Lily are also very good. They're inspired by classic RPG Maker horror games and about kids going to the demon world to solve their problems, only to subsequently realizing how horrible of an idea that was.