Princess Waltz is fairly unique among Visual Novels by actually providing character models for the random classmates, most of which are Those Two Guys. Most notable are Nodoka (Cute and Perky) and Kazuko (Talkative and Loud). In a twist, one of the even more minor Those Two Guys turns out to be the Secret Identity of a fairly major character.
In Tsukihime, there is only "That One Guy" (Arihiko, who has this going on with Shiki, the main character, before Shiki becomes an Ordinary Highschool Student), though his role is exactly as in the trope.
Arihiko is further unusual in that he's surprisingly well-developed for a supposedly minor character. He even gets his own Day in the Limelight story in Kagetsu Tohya.