Ever17 -The Out of Infinity-Tsugumi is bae. A great VN, despite the "No Sexual Content" tag. Tugs at the heartstrings, especially during the washingmachine part.
Fate/Stay NightRin, why are you so best? Good soundtrack, interesting characters (I personally liked Shirou excluding Fate route) and great battles. UBW > HF > Fate.
Grisaia no Kajitsu -Le Fruit de la Grisaia-Not your typical harem. All girls are good, but Sou Amane is a best. Yuuji is also a very great protagonist. Worst thing about this is the OST, but it has a few good tracks.
G-senjou no MaouFor those who enjoyed Death Note or Code Geass, this one's for you. The most deserving of the "Battle of Wits" tag, and also boasts one of the better OSTs. Only one real route though, the rest were more or less tacked on. That being said, best girl is true route so that doesn't matter.
Kamidori Alchemy MeisterThis is both a game and a VN. Sexual Content doesn't come immediately, but when it does, it does so quite spontaneously. I haven't finished it yet, but it's a good game nontheless.
Muv-LuvGeneric, but by no means horrible. There's quite a bit of foreshadowing even in the harem parts of this VN. Sumika a best.
Muv-Luv AlternativeI adore this VN and implore that everybody gives it a chance. It has a wonderful combination of great characters, a beautiful OST, and an emotional story. If you put effort into reading Muv Luv Extra/Unlimited, the impact will be that much sweeter. Remember: You can only experience it for the first time once.
Sengoku RanceRances is a arrogant, selfish man who will rape any woman who catches his eye. Still not that bad compared to some of his foes. A simple but fun game with lighthearted rape and many a good girl. Kenshin, of course, is a best tho.
Sharin no Kuni, Himawari no ShoujoGreat protagonist and an interesting setting. Story isn't particularly good, but Sachi is great and that is all the matters, yes? Just CTRL through Natsumi's existence and you'll be fine.