From my little experience in VNs, my favorite 3 OSTs are:
3: Grisaia No Kajitsu. Some of the soundtracks got me completely into the scene to the point where I could not stop playing. Especially the dramatic/creepy ones.
2: Katawa Shoujo. This was my first VN, so it holds a special place. I find it hard to find a single song that wasn't at least 'good'. Some of the songs I still listen to and enjoy on a regular basis.
1: Little Busters!. Little Busters wins on feels factors. All of the soundtracks have some sort of amazing memory linked to them. They are happy, sad, scary and whenever I listen to the vocal songs I am always overwhelmed by feeelsss and find myself wanting to replay the game.
This said, I still have a lot of VNs to read.