Unlike the anime, which began with Shion escaping the school in record time
, the game's first hour or so was spent with Shion in the process of sneaking out while avoiding guards and getting through locked gates. Shion paused shortly after the game started, and began describing her situation, how she ended up in this quiet suburban boarding school in the first place, and why she's breaking out.
The track played during this scene was "Iru". Which, despite being merely 1:25 long, is one of my most favorite, if not the most favorite, track in Meakashi-hen. The track had a very calm and nolstalgic melody to it, and fitted the night scene perfectly.
After Shion escaped and met up with Kasai (the sunglasses guy, who is Shion's bodyguard), they headed out onto the highway to return to Hinamizawa. At this point, the game's logo appeared, along with the "opening song", which is "Thanks".
The meeting between Shion and Satoshi was also accompanied by one of dai-san's great tracks. I don't remember if it was "Thanks" or "you" though.
Tsumihoroboshi-hen featured some great tracks as well (not just from dai-san), so it's a slight disappointment that we won't hear them in the anime.