I haven't read very many yet since it's difficult to find any good translated titles in the genre I'm into, but here are my top 5 for the PC nonetheless, descending in the order from last played to first played.
1. Kara no Shoujo
Although I'm somewhat saddened that they killed off one of my favorite characters and left the canon ending unresolved, it was great and got very disturbing during the murder scenes.
2. Umineko no Naku Koro Ni
Although I didn't enjoy it as much as Higurashi, it was still mind disturbingly awesome. I'm still waiting for Ep 8 to finish translating so that I can move on to Chiru since I don't want to get the game twice.
3. Higurashi When They Cry
Still one of my top 3 visual novels for the PC simply because of how it was pulled off. At first I thought I was playing some sort of slice of life game, only to find out the cruel fate that awaits everyone later. Though as a mystery lover, I didn't like how
they didn't explain why Keiichi and others were able to know something from a parallel world.
4. Fate/Stay Night
I liked this one a lot the first time, but for some reason I can't get myself to read it all the way through again a second time like I did with the others. Still, it was good even after Higurashi and others came along.
5. Tsukihime + Plus Disc and Kagetsu Tohya
My first visual novel and probably will be my #1 favorite for a long time. Although the writing is outdated by the more modern vns, I still consider it my #1 particularly because of Hisui <3, it was the vn that got me to look for more for the PC, and I also really enjoyed all the heroines' backstory as well as their route and endings.
As for my top 5 on other systems outside the PC, here are mine in the order from most favorite to least:
1. Ace Attorney series
The games that got me into the genre in the first place
. Although I see it more as an adventure game rather than a visual novel now, the fact that it plays like one is what appealed to me most when I first got it since it was a nice change of pace from RPGs and whatnot. All the finger pointing actions in the court room and pop cultural references really makes it one of the best series in this genre out there.
2. Hotel Dusk + Last Window
I really liked how they did the character animations in this one, as well as the art style. Not only does it bring out the game's noir-like atmosphere, but it was very unique and well-pulled off. The story makes the games even more wonderful since it keeps you on your toes, wondering how everything is going to turn out.
3. Nine Hours, Nine Persons, Nine Doors
I thoroughly enjoyed the story, the characters and the atmosphere in this game, even if a lot of the mathematical puzzles gave me a huge headache. I was always on the edge of my seat wondering what will happen next, considering anything can happen in their situation. I'm hoping the sequel will be just as good.
4. Famicom Tantei Club II
One of the very first visual novels I've played right after Ace Attorney's Justice For All, and it was on the SNES! I really liked the twists they provided throughout the game, as well as how discreet the criminal kept themself from you. Though, it's a shame that I will probably never get to play the first one (In which the story takes place after this one) due to lack of a fan translation.
5. Time Hollow
Well, I didn't really know what else to put here but yeah. Despite how little use you get out of the hollow pen, the game and its story was still interesting to read. One of my friends enjoyed it greatly even though he never got the chance to finish it, and he's never read any visual novels before.
Nothing to see here, folks. For now, anyway...