Conveniently Seated

When a scene takes place in a classroom, the Ordinary High School Student tends to be located wherever is the most convenient for the author, plot, or characterisation of the character.

Often near the window, so the character can be showed looking outside in dreamy fashion. Or near the aisle, if direct personal interaction with the teacher is needed. But then still on the end of the row, with only the window seat between the character and the end of the row.

If the teacher doing his teaching is an important part of the plot, the teacher will be sitting on the middle of the front row, so that a shot can be taken from behind the main student cast, facing the teacher.

If the focus is on the students, they will be sitting on the back row. This way, the author doesn't have to portray everyone sitting behind them. But not too far back: In order to still give the idea that they sit in a larger class room, the gang will be sitting on the second from the back row. Conveniently Seated also applies to settings such as movie theatres.

In Anime, the second seat from the back, along the side with the windows (which is always the left-hand side of the classroom) seems to be extremely popular.

Anime and Manga

 * Seating in Mahou Sensei Negima:
 * Sayo near the left corner window-seat so she can stare wistfully at freedom; her friend Asakura so she has a good view of the room, giving her the best ability to take pictures.
 * Chisame and Yue in the far back and middle to observe the stupidity of their class; Haruna is next to Yue because the two are librarians.
 * Ayaka in the front and middle to best serve Negi-sensei. It also gives her a commanding air.
 * Evangeline sits in the only desk that makes up the fifth row to the right - helps her sleep in class and not get called on for questions; Chachamaru in front of her to be as useful as possible; Hakase beside Chachamaru to easily repair her when necessary (in other words, the last two sit where they do to be convenient to Eva).
 * Asuna and Konoka in the second to back and middle to effectively be in the center of the room. Being room-mates with The Hero warrants this sort of placement.
 * Zazie in the corner, in order to be on panel the least amount of time as possible, to add to her mysteriousness.
 * Neon Genesis Evangelion: Rei gets the symbolic window seat.
 * MM: Taro Sado: keeper of the seat in the second row back, along the side with the windows.
 * Death Note: Light also gets the symbolic window seat, and it also gives him a great view to the yard where the death note gets dropped.
 * Durarara's Meaningfully Named Mikado Ryugamine gets a window seat that's in the second-to-last row. A minor character, Rio Kamichika, also has a window seat from which she can stare out wistfully and contemplate the world and its many odd inhabitants.
 * Kyon from Suzumiya Haruhi No Yuutsu ends up near Haruhi. In the Suzumiya Haruhi novels they also keep changing seating positions (to keep things fresh, to Kyon's scepticism), which doesn't stop him from being right by Haruhi. They both sit along the left-hand windows, in the last two rows of the class.
 * Yuiichi, in the more recent anime adaptation of Kanon sits in the second-to-last seat along the left windows. Three of his closes friends, including his cousin, all sit in the three seats directly adjacent to him.
 * Keiichi, the main character of Higurashi no Naku Koro ni always sits in the second-to-last row, along the windows. The girls in the series all sit next to him as well.
 * Azumanga Daioh: Sakaki is planted in the window seat and a majority of the main cast sits in the next row over, with Tomo situated on the opposite side of the room. Most conversations in the show tend to happen towards the back of the classroom, near Sakaki's desk.
 * Natsume, the protagonist of Natsume Yuujinchou, sits in a seat by the window between his friends, Kitamoto and Nishimura, and is usually shown looking outside during class time, thinking about his most recent Youkai experience.
 * In Cardcaptor Sakura, Sakura is in the ever-popular window seat, with Tomoyo next to her, Shaoran behind her, and Meiling and later Eriol behind Tomoyo.
 * In K-On! the main character Yui Hirasawa sits in the window seat in the last row of the classroom and the drummer Ritsu Tainaka sits in front of her.
 * In Bakuman｡:
 * In first chapters, Mashiro sits in a row behind Azuki's, which gives him an oportunity to observe her during the class and thus draw a sketch of her in his notebook.
 * Takagi's seat is in the back row, which gives him an oportunity to observe all his colleagues and notice how Mashiro looks at Azuki.
 * Then, after Mashiro and Azuki promised to each other that they will not meet until they fulfil their dreams, a big shuffle happens which puts the two of them seated at the same desk. Cue the embarassed looks on their faces and Takagi (who is again convenently seated in the back row) almost bursting into laugh.
 * In Its Not My Fault I'm Not Popular, when the second semester starts and Tomoko loses her back row seat by the window, she lampshades it by commenting about how lucky she was getting "the seat main characters always get in anime and light-novels" in the first period, lamenting that she now has to dwell in an awkward spot, surrounded by people.

Web Comics

 * Pointed out in El Goonish Shive here, as seen above. Read the line of text below the lowest panel...

Western Animation

 * Timmy Turner sits in the first row (along with his two best friends) right in front of Mr. Crocker.
 * Bart Simpson sits by the window, if not required otherwise by the plot.
 * Batman Beyond has a tendency to show Terry and any other important character (Max, Dana, Nelson, etc.) in the front row, no matter how improbable it is that they would choose to sit there. Perhaps assigned seating?
 * Beavis and Butthead sit in the middle of the back row in every class, with nobody else in that row and their desks out of line with the rest of the class. It saves a lot of trouble having to constantly animate people around them, presumably.