LiquidText PDF Reader is a unique app free app that lets you read and annotate PDFs actively and visually. The latest updated improves the color palette choices available for highlighting text and commenting.
Not only can you highlight, but, once the text is highlighted, you can press and slide the highlighted text to the side and organize your selected text pieces.
You can pay for an in-app purchase for $3.99 that will allow you to work with multiple documents simultaneously.
If you are looking for an great app to annotate and read your PDFs, check out LiquidText PDF Reader.