I'd like to preface this by noting that I understand that my district's school lunches are considered particularly good, and the examples I give are not always the case elsewhere.
As I mentioned previously, the Japanese education system encompasses more than just academics and extends to all aspects of life, with every moment of the school day used to impart some sort of lesson. Naturally, that includes the lunch period, particularly in elementary and middle schools.
Kyushoku (給食), or school lunch, is provided in nearly all public elementary schools as well as in middle schools outside of the more urban areas (this, of course, includes mine). The contents of each day's lunch are determined by a nutritionist and include a wide variety of foods in varying combinations making it so that the same meal is rarely served twice. A normal lunch will have a main starch (generally rice, though occasionally bread or noodles), a vegetable side, a main protein, a soup, and a carton of milk. Though the healthfulness of the meals vary, they're nearly always relatively well-balanced, if not a bit calorie rich (they are made for active, growing adolescents, after all).
Lunch is prepared daily by a kyushoku center that serves all of the schools in a district and is delivered via truck just before noon. The school's custodian (normally an older woman whose job it is to upkeep the school) greets the truck, prepares the teachers' meals, and readies the food containers for the students. Once fourth period ends, the students whose turn it is that day dash over to the loading area to begin lunch service.
Some schools have lunch rooms and some just eat lunch in the classroom, but in either case the process is much the same. The students will don aprons, hats, and masks, wash their hands, and begin wiping tables and setting out plates. Rice and soup are scooped into bowls at the front of the room before being distributed, while the students in charge of the vegetables and protein will walk around the tables, serving each place individually.
Like souji, this is supposed to promote responsibility as well as encourage other important values like impartiality, cleanliness, cooperation, and punctuality.
Another important lesson kyushoku is meant to impart is healthy eating habits. Everything that the students consume during school is pretty tightly managed. Unlike in most American schools, students aren't allowed to bring snacks from home, and even if a teacher wants to do something in class with food, they need to get special permission to do it first. Students are also made to finish their entire lunch regardless of likes/dislikes, even if it means sitting behind while the rest of the class cleans up once eating time is over.
At first I was more than a little skeptical about how strictly food is be controlled. But there do seem to be positive points as well. For instance, I imagine this is pretty good at teaching portion control.
While the protein/main dish will all be the same size, all of the other portions are tailored to each student's appetite (to an extent). In middle school you'll see a huge variation in amounts of food ranging from half-full bowls of rice for the girls with the smallest stomachs, to bowls piled high with two servings for the third year boys. If a student is absent, their portions are distributed among their classmates, and the hungriest boys will rock-scissors-paper fight for the things that can't be so easily split (think whole fish or cartons of milk). Other than that, though, there isn't really much moving of food between plates.
In elementary school, students have the opportunity to ask for more or less of certain dishes before everyone begins to eat, and if there are leftovers the ones who finish their food first are allowed to ask for more. However, exactly how much they get to increase or decrease their portions is left up to their homeroom teacher, as at that age sometimes eyes can be bigger than stomachs.
Something else that I noticed was that these kids, even the youngest ones, are so much more knowledgeable about foods than their American counterparts. And a lot of that probably has to do with the incredibly wide variety of foods that they're exposed to on a daily basis. Rather than a menu that stays exactly the same month-to-month (as was the case in my own elementary school experience), the dishes are highly dependent on seasonal ingredients. Foods outside of the normal spectrum of Japanese cuisine also pop up regularly, the most common of which are Chinese and Korean-inspired dishes, with the occassional "Indian" curry thrown in (though Japanese interpretations of foreign foods leave much to be desired, but that's another problem for another day).
Though of course, things differ from region to region, and I'm sure that rural areas tend to benefit a bit more. For instance, my area is a farming/fishing town and has a lot of readily available, locally produced, seasonal ingredients that are used in kyushoku every single day. At one of my schools, their district's kyushoku center goes so far as to note exactly which farm each local ingredient comes from.
There's also just a lot more education about food and nutrition in general. Once a month or so, either the school nurse or a representative from the kyushoku center will do a short presentation on some aspect of nutritional health for the students. And every day's lunch comes with a short blurb about one aspect of the meal, be it a certain ingredient that's featured or a preparation style that they might not see at home. At my middle schools, there are also days set aside specifically for the students to make and bring their own bento to school.
October just happens to be the prefecture's food education month, where an even higher than normal proportion of local ingredients are used including Tajima beef. For those not in the know, Tajima beef is both Kobe beef and Matsuzaka beef, the two top quality types of beef in Japan. The cattle that become both types are born and raised in Tajima (this area!) and then shuttled elsewhere to be...processed and are subsequently renamed. So basically these kids are getting Kobe beef in their school lunch.
This month's menu also includes six days featuring locally caught fish (which is about standard every month), as well as the much dreaded, once-a-year appearance of deer meat sausage, made specifically to deal with the growing deer infestation in the area. Seeing as it's the least popular menu item, the kyushoku center made a good call pairing it with Japanese curry, a fan favorite that is also very strongly flavored.
People seem to be particularly interested in the topic of kyushoku when asking about Japanese school life (for good reason, food is easy to relate to, and Japanese food is famously delicious) and are always really impressed when they find out all of the above. And I agree, kyushoku is rather idyllic when compared to the school lunch situation at most American public schools. But that doesn't mean it's without its flaws.
For one thing, forcing students to eat all of their food even if they don't like it is a great way to make them hate that food for life. And the fact that you either get kyushoku every day or not at all leaves little room for students to avoid that situation. Furthermore, while kyushoku is markedly more nutritious and healthful in general than American school lunch, it often includes things that are definitely not healthy such as things that are deep fried and cream-based stews. Vegetables do appear plentifully every day, but because of Japan's bizarre fear of food-borne illness (the reason you're not allowed to take home your leftovers from restaurants, fyi), they're never raw and are usually boiled to death. And of course there's the fact that the quality of the food is highly dependent on location and funding. So it's not quite the shining beacon of light and nutritional perfection that baffled American journalists make it out to be.
If you want to learn more, I recommend reading this post by Maki of Just Bento. She talks about kyushoku a bit more, and the comments are full of interesting anecdotes of school lunch experiences in Japan and elsewhere.