GoodReader, NYT Editors Choice, and iBooks.
Brief rant - Getting content on and off the iPad is clumsy, file management is worse. Apple should try it some time, then come up with a more elegant scheme. iTunes works sometimes, and it's nice they added the ability to add files to apps through iTunes, but it gets ugly fast with a lot of files. Plus, each app has to manage it's own files. Very messy.
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