Very little. I take this usage to refer to the school building/grounds and whether the verb or noun in the rest of the sentence is actually inside the building (in the school), somewhere on the school grounds or even very near the school property (at the school).
Take away the article: at school/in school, and things get a little more complicated.
If I understand my books, one usually uses "at" if one wishes to put the emphasis on the location of a place; one uses "in" if one wishes to emphasize the interior of the place.
1. (I made up this example) The students are going on a trip to the mountains tomorrow. They have been instructed to meetat the school by 7:30 a.m. in order to board the buses, which will leave at exactly 7:50 a.m. Late students should return home. [Do you notice that "at the school" simply refers to the meeting place?]
2. I found this quotation in Google "books": "It was thought to be a mark of high efficiency in the school to fail a large per cent [sic] of the students." -- Report of the School Survey (1916).
[I think that you will agree that in this case, the location is NOT being emphasized. The activities within the school are being emphasized.]