As advanced as they are now, digital devices still can't beat paper and pen(cil) in notes taking in many people's book. There are certain experiencial elements that can't be replaced when writing on a paper holding a pen in your hand. However, digital devices can definitely help people gain more value out of the notes just on paper.
Pieces is an iPad app concept design for documenting notes and help reveal patterns and find connections among the notes.
Pieces Concept Prototype (02:29).
Pieces: timeline view.