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You could also email them to yourself. When you open the attachment on your iphone it will allow you to launch the PDF in iBooks. Also, a good app for opening documents, GoodReader, also allows you to open the stored PDF in iBooks.
 
Wirelessly posted (Mozilla/5.0 (iPhone; U; CPU iPhone OS 4_1 like Mac OS X; en-us) AppleWebKit/532.9 (KHTML, like Gecko) Version/4.0.5 Mobile/8B117 Safari/6531.22.7)

You can also open PDF links in safari and they'll load in iBooks
 
If you have an actual ebook in PDF format, it may be difficult to read comfortably by adding it to iBooks via the suggestions above.

You can use a software program called Calibre to convert a PDF to an epub file that when synced to your iPhone will read in itunes like a book normally would, with options to resize the text etc.

http://calibre-ebook.com/
 
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