The house system is well-established in British schools, and goes back hundreds of years. It originated (and was most common) in boarding schools like Hogwarts, where the students live on the school grounds, and the houses they're sorted into are the houses in which they actually live. Again, just like Hogwarts.
It's worth noting that the popularity of Harry Potter has actually caused house systems to become more common in British schools, especially "day schools" (the regular kind of school where you don't live on campus). The secondary school I went to initiated a house system in the year I started there, and just like Hogwarts, the houses were blue, green, yellow, and red, and had animal-themed names. So it's usual now, but I wouldn't say it was usual at the time Philosopher's Stone came out. It just so happens that Harry Potter caused the house system concept to explode in popularity over here.