I've tested and looked at a number of apps to use on the iPad to read articles and books in PDF format. Of these, I think PDF Expert is the best:
1) It has best designed and simplest interface for highlighting and annotating documents. My view is that the iPad is a great platform for reading electronic texts (vs. a desktop, laptop, or eInk based reader) because its design is such to facilitate a very transparent and intimate engagement with text (for an electronic device). eInk is intolerably slow for quick scanning and reading, desktops are too remote and immobile, laptops too heavy and hurting of fingers and wrists around sharp edges. (Of course paper has the benefit of making present the whole article or book at once, of giving you a visual-physical-tactile map and sense of the whole thing and where you are in it; an iPad is never going to fall open just at the right page, or dogear you in the right direction.) Once you are engaged with reading on an iPad, transparent and engaging, clean design becomes a premium. PDF Expert has this: fewer steps to highlight, or enter a note on text than the best runner up Good Reader. E.g., PDF Expert automatically positions the flag for your sticky note text in the margin, and it's got a better interface for repositioning these flags. It's really quick to read through an article or book, highlight important passages with your finger, add notes if you want. And then it has a nice interface for looking through notes, highlights, bookmarks, etc.
2) File manager: GoodReader has powerful functionality for getting files on and off the iPad, but it's incredibly byzantine. PDF Expert's file manager interface is clean, clear, easy to use, transparent in function, and powerful, esp. it's ability to use SugarSync, so you can sync with PDFs on your computer.
3) It's also easy to open PDFs in PDF Expert from your email or web browser
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