The iPhone does not allow you to take PDF documents with you on the device. You can view PDF files on the Internet - which means that you need an Internet connection. But what do you do if you are flying? or going to an area without any wireless signal? (Personally, I would want to take the Colorado fishing regulations booklet with me when I go fishing in Rocky Mountain Nat'l Park).
One way is to JailBreak your iPhone - but that is not an option that I am particularly fond off.
Another way is to convert your PDF into a special type of a web link (URL) called a URI. (link). Again I am not fond of this approach as there must be a data size limit on how much the Safari can handle as part of a URL.
And I found the answer in Files, an iPhone app. (link). It not only allows you to store PDF files, but also a variety of other ones like: Word Docs, Images,etc.
I haven't yet tried the app, as it costs $7.99. I wish it were free or had a try before you buy option. But it has all the features I would have wanted in such an app and more. Files is available for both Windows and Mac machines.
FileMagnet: this is another App that allows you to copy and view files on your iPhone/iPod Touch. But it works only for the Mac. (it is also cheaper at $4.99)