Top 5 with my personal thoughts
Not necessarily in order
1. Fate Stay Night (No need for further comment i believe)
2. Kanon (Nayuki!.. Can't get enough of her.. And storywise, it's KEY, and that said everything.. You can even feel the coldness of it's winter atmosphere.. Not to mention, the musics are top notch)
3. Snow Sakura (The first VN that taught me that even a typical heartwarming friendship, family, and love stories can hit the spot.. Such a warm story packed in cold winter theme.. Definitely one of my favorite legedary VN)
4 and 5 suspended.. Got tons of considerable candidates, and i can't choose yet..
And..
1. Fortune Arterial ( The very first VN that can even be brought into my dream!.. Seriously!.. I took the protagonist' seat in that dream)
2. Tayutama series (Kiss on My Deity and It's happy days)
3. To Heart 2 X Rated
4. Yoake Mae Yori Ruuri iro na
5. Shuffle!
I'm sure about my top 3, but the rest aren't.. Since there are like more or less than 100 VNs that i've played, most likely i missed the name of some awesome VNs..