Obie's notebook is "more complete than the school's files. It contain[s] information, carefully coded, about everyone at Trinity, the kind of stuff that couldn't be found in official records" (2.45). It's also where Obie records Vigils assignments, as well as the names of students chosen to carry out the assignments. The book is literally filled with symbols (writing, code) of what The Vigils are up to. Put all this together, and you can say that the notebook is a symbol of The Vigils' crimes.
We might also see Obie's notebook as a symbol of his talent, and how this talent is being warped by the Trinity atmosphere. In a healthier environment, Obie's skills – keeping good records, organizing, and writing in code – could be used for good. But, at Trinity, strengths are twisted into being used for evil purposes by The Vigils and the school administration. Take a step back and you could interpret the notebook as symbolic of every student whose potential for good is being perverted by the unhealthy atmosphere at Trinity.