Annotator is the best pdf-only app I've found:
- Supports browsing via outline (that's the contents you see in the sidebar in Preview), page number and bookmarks (which you can add yourself on the iPod).
- You can search the pdf files, the Annotator uploader indexes each file before it zaps it to your iPod.
- You can annotate the file directly on the iPod and have those sync back to the files on the computer.
It's pretty cool. PDF files only but damned good at what it does.