In yWriter, the concepts of character and scene are baked right in. It's designed for fiction, and it's a fine tool when your style fits the structure it knows about.
I tend to prefer tools that allow me to evolve my own structures, without trying to help by constraining me to its known templates.
Scrivener helps you organize your text (and ideas) into a hierarchy of chunks of text. It has no preference for what size chunks, or what you call the chunks. If you write a novel, you might have chapters that have scenes. If you write a technical document, you might have parts that have chapters that have sections that have subsections. Scrivener don't care one hoot. You decide the meaning of the hierarchy.
Super Notecard (from Mindola) is another program that allows arbitrary chunks. It also knows a few things about research, such as citations, in a way that gives just a little bit of help, without imagining that it knows more than you do about how you want to organize things. I remember liking it once upon a time, but I find that Scrivener somehow fits me better. It's been a while since I compared, so I don't remember the distinguishing details.