Annotating, marking text, taking notes, marginalia notations, underlining, highlighting, starring, or using the current "sticky notes" all have something in common: personalizing a text. The reading of a text is a personal relationship, and therefore the marking or referencing of specific content is a personal conversation between reader and writer. Therefore, since this is a unique relationship, whatever is chosen by you, the reader, is uniquely your own.
So how do you "know" what quotations to choose? Think about the purpose of your reading and what will be the outcome of this process. If an essay will be assigned at the completion of the reading, what will the essay ask you to discuss? If discussing universal themes of a work, pay attention to potential big ideas. The sticky note will save time later as it enables a reader to come quickly back to a specific point in the novel in order to reference during discussion or writing. If discussing a writer's style, pay attention to figurative language (creative use of simile, hyperbole, personification, and metaphor), or perhaps interesting sentence structure.
Simply, when a line, word, or grouping of words speaks to you and causes a pause in your reading, it is because you are in essence conversing with the writer on a more personal level. Mark it. Underline it. Star it. Or simply "sticky note" it.
I think that this might be a question that can be approached in a variety of ways. Certainly, readers who have read more and gained a certain maturity in their ability to read can identify particular quotes to "sticky note" and be able to explain with their own skill set why those quotes are meaningful. From a student point of view, I think that that you are able to identify which quotes to sticky note, in large part, through class discussion or instructor analysis. As your instructor or discussions about a particular work develop and take form, you might be able to "sticky note" quotes that expand a certain idea that was previously discussed, or enhance the dimensions of a certain character or conflict. Much of this comes from being attentive to what is being discussed. If you are not experiencing this, I would say being able to "sticky note" quotes or passages that reveal much about a particular character or conflict, a specific style of writing, or a motivation of either character or writer would be strong justification to "sticky note" quotes.