Hi, I bought the ipad a little while ago with the intention of using it almost solely as a PDF reader. I have thousands of pdf papers, text books etc, and I'm looking for a decent program to organize them all. I've read a lot of online reviews but they don't seem specific to my needs. I downloaded "PDF reader" which was not the best program (and it was 4 bux...). Here is what I need in a pdf reader, hopefully someone knows the ideal program, or can make one! 1. Program must handle thousand page pdfs 2. many PDFs have links to chapters etc within them, I need the program to maintain these and keep them functional. 3. Easy transfer from computer to ipad. With "PDF reader", you cannot import folders of PDFs, so I currently have a mess of thousands of pdfs all mixed, while I would ideally like to be able to copy the folders to maintain the organization. 4. Ability to download and organize pdf's directly from the web. I commonly want to save some articles I'm reading, but "PDF reader" (despite claiming it can do this), cannot do it from the site I use. (I am trying to save mainly scientific papers which require access via my university website). 5. Good bookmarking options to keep track of where you are in multiple documents. 5. Cherry on top, but the ability to make notes or highlight/circle things within the pdf for future reference. Next, a lot of my text books are in the dreaded .CHM format. I tried to convert some of them to pdf but the final copies are terrible- poor formatting, no chapter links, essentially unreadable, especially since they are about 8000pages of unformatted text/pics. Any help is greatly appreciated. Thanks.