Art...
My top pick will always be Sanguine Rose. I love her art, I think she's incredibly talented.
Depraved Awakening comes second.
Roundscape Adorevia takes my third. I know some people don't like the inconsistent styles but for the most part there is some gorgeous artwork in that game.
Clare's Quest. I'm not the biggest fan of the game in general, at least I wasn't until the futa scenes (normally not a fan of dick but the scenes there just did something for me) but the art is beautiful.
Fifth will be Fate of Irnia. I adore this game and the art but it's a shame the Dwarf was cut before we got to know her. Still, I get Lady Death and the sexiest Orc since Rucksana. What I wouldn't give for a little lesbian Orc harem....
Story...
Last Sovereign is my number one. One of my favourite games. It's not so much as the story has anything revolutionary but the way she tells it along with the characters and world building, it's had me hooked since I first picked it up and it's one of a very short list of games I need to play every update.
Sanguine Rose gets second here. I don't know if it's a married couple or just friends but her art with his writing made this one of the best Visual Novels i've ever had the pleasure of reading.
Another Sierra Lee game (i'm a bit of a fangirl of hers) with Desecration of Wings. I adore this story and it's characters. So many games make women out to be sluts that like sex yet here we have a woman that loves sex, works as a prostitute and is a total badass to boot. I love Felana and I love the game.
Roundscape Adorevia. It's another one of those games that does nothing we haven't seen before but how it's told along with the characters being likeable hooked me pretty quickly and keeps me coming back.
Mutiny. This is on here because I love the theme and this is probably my favourite game. It's not a massive story but it's told well and the banter is spot on along with Grace who is the best character i've ever seen in a game.