The iPhone's Mail reader allows you to read small PDFs with its built-in viewer. However, it's a bit limited, and it also requires you to e-mail the PDF via e-mail and download it from the iPhone. This might be quite problematic for large files, right?

PDFviewer is a native third-party application that comes to rescue. You can get it through the Installer app, browsing under the Community Source. To upload the PDF files you need to SSH into the iPhone (refer to this FAQ if you're a Windows user, and to this FAQ if you're a Mac user) and put the files under the private/var/root/Media/PDF/ folder. If the folder does not exist, create it (note that the folder name is case sensitive though). Finally launch PDFviewer, and it will list all documents found under that specific folder. Tap on one to read it.