iAnnotatePDF for iPad is down to $2 from $10
If you work with big PDFs a lot, this app is great. I can't compare it to GoodReader or PDF Pen, but I will say that when I was in school reading long journal articles it was my best friend. My favorite feature was the full-text searchable bookmarks — you can write notes in the book then show or hide them when you read through the next time, jump back and forward, and use them in addition to any bookmarks that are already built into the PDF. It might not have the most intuitive interface, but I'd recommend it at $10, and at $2 it's an absolute steal.