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Write down things that stand out to you while you're reading. If something is worded strange, point it out. If a statement is ironic, write it down. If a word is repeated several times, take note of it. Usually when you are annotating you are looking for implicit meanings, so it helps to engage yourself in the reading by thinking about what the author's intention was in writing the way they do. When you are trying to figure out what the implicit meanings are, you can reference the different annotations to help you figure it out.
annotating is a form of interactive reading. it is more than just highlighting because you are taking into consideration the actual content of the text. When i annotate I summarize what the author is drying to say. Or I will challenge a view point that I don't agree with. The point of annotating is to be able to go back into the book and not feel completely lost because all it looks like is a bunch of words. Annotating things such as syntax, ethos, pathos, metaphors, similes, and anything else that has significance can help in the overall understanding of a text, as well as help you draw specifics quotes into any assigned essay.
I agree with the two about, if you have a variety of writing techniques, make sure you point those out, and also say what effect that has on the reader. Make sure that you highlight words showing the mood of the text and key quotes that determine the text too!