I haven't worked with paper in a long time, but IIRC some notebooks I used in school had pages you could tear out, sacrificing a strip along the side, while preserving holes that'd work in a 3 ring binder. So then you could just write anything in one of these notebooks, tear it out, and put it in a 3 ring binder afterward. The binder could be more thematically organized then, separate binders by subject. A bit like opening your text editor, writing stuff down, then deciding which dir to save it to later.

Also even if your paper doesn't have the holes, you could use a punch to add them, assuming you have space on the side without writing.