Is there an iPhone App for reading PDF files?
GoodReader is very handy. You can wirelessly transfer files and you can even add any web content to the GoodReader library simply by placing a "g" in front of the URL in mobile Safari.
As of 21st June, the Apple iBooks app can read and bookmark PDFs.
My wife uses Evernote to read her existing PDFs of her knitting patterns on the iPhone - plus she has the benefit of them being available on the web, and her laptop. It also has a great free version.
I use Air Sharing which creates a virtual drive on your wireless network. I can copy files (including MS Office and PDF files) to my iPhone and view them. There are other file transfer apps that do similar things.
If you're starting with documents that are not PDFs (e.g. Word files), you might find reading PDFs inconvenient since PDFs are inherently page oriented. Stanza's FAQ page has an answer about creating ePub content from other documents.
Readdle has an iphone app that allows you to download files in many formats from the web to your iphone. They give you some free storage space at their site, but you can sync the files to your phone for reading on a plane, etc.