A lot of what is seen in anime relating to school life is drawn from the writer's memories of *their* life in school -- so you need to subtract 5-20 years. OTOH, the system and the students change rather slowly so lot remains consistent. About the biggest impact to school life that is only recently being portrayed in anime is the overwhelming social changes due to cellphones. Uniforms are still the norm rather than the exception --- though the flamboyant uniforms seem to be less popular.
Recently the Japan education system has finally (about 10 years too late) started to grapple with the problem that cellphone usage has become a huge distraction from the educational process. There are movements to ban cellphones on campus --- though imho some updates to the teaching skills and process might be more effective :P
