Aside from spellbooks, as noted, you can discard, destroy, or sell (usually for a single gold) any document that gives you the option. Or you can keep a library in your inventory or in a convenient box or bookshelf. Nothing goes away unless you destroy it.
Some of them are useful later, though, and the game leaves it up to you to decide which are which. It's very open-ended, and doesn't do much hand-holding.
As a general rule, though:
- You *are* investigating a murder, here. If you find a book or other document where the characters talk about it, there's an experience award, and a journal entry; do you throw away what appears to be relevant evidence, or do you keep it to use later? After you're sure you're done with it, what do you *want* to do with it?
- Books can provide useful reference information for a current or later quest; can be actually needed to do something in a current or later quest; or may just provide color and ambiance. There may be no experience award or journal entry, and the characters may have nothing to say. You get to decide what you think you should do in each case.
- You may choose to look into crafting scrolls and spellbooks. Blank parchment, or notes that are no longer useful (or never were) may be of some use to you in this endeavor. Haven't tried using maps: I usually read them and then sell them right back, because my character is a bit of a prick like that. Role-playing! It's all role-playing, I swear! You believe me, right?