Skim is a PDF reading and note-taking app for Mac OS X that is designed to make reading research papers and manuals better. Just like in Preview, you can search, scan, and zoom through PDFs, but you also get some custom features for your workflow:

Snapshots

If there’s a graph on page two and the description continues to page three, just draw a box around the graph with the command key down and a snapshot window pops up with the graph, and you can keep on reading with the graph in view. For more fun, minimize that snapshot window - they stick around in their own dock in the document window.

Tooltips

If a PDF has links, such as for citation references or indexes and section headings, you can click on them as usual to go to the destination, but there’s more - hover the mouse over those links and Skim will show you a tooltip with the target of the link. No more losing your place to peek at a citation! For more fun, command-click on a link to pop up a snapshot window showing the link’s destination.

Presentation and Full-screen Modes

Full-screen reading is handy. So is showing a PDF as a presentation. But they’re a little different. For instance, you might not want to show the table of contents in a presentation, but it’s nice to see it when you’re just reading by yourself. So Full-screen and Presentation are separate modes in Skim.