Hi Rob,
I think I've found a new feature in iOS4 that I can't find mention of anywhere on the web. When opening a PDF in Safari running iOS4, a black bar appears at the top of the screen with a tab that let's you 'open in iBooks' so that it is saved to the PDF section and is viewed in iBooks.
This feature is not present on my iPad running 3.2.2.
It is very handy since I often load PDF files on the go and want to save them. This feature hopefully makes it into 4.2 for the iPad. Using different PDF Apps is annoying and unifying this within a native App makes sense.
Matthew M