I think GoodReader (iTunes Link) is right up your alley.
It supports PDFs primarily, but according to it's site also supports Microsoft Office, Apple iWork, HTML WebArchive, images/audio/video files.
It can connect to Dropbox shares, download resources directly off the web (and some other protocols, FTP, SFTP, WebDAV) in-app, supports Document Sharing (file loading via iTunes), features autoscroll, and many many more features and customizations that you didn't ask about!
It is unfortunately NOT a Universal app, USD$5 for the iPad version. And another USD$5 should you ever want to buy it for an iPhone/iPod.