Squid (formerly Papyrus)!

Notability is the first truly integrated note-taking app for iOS. Standing on a framework that automatically links notes with audio recordings, Notability supports all of your note-taking needs -- handwriting, PDF annotation, word processing, and more work together seamlessly allowing you to create comprehensive, beautiful notes, quickly and simply. Auto Sync ensures your notes are backed up safely. And now you can personalize the look and feel of Notability’s library and toolbars with Themes, from colorful, to clean, to classic. »

GoodNotes lets you take notes and annotate PDF documents. They will be synced to all your iOS devices automatically, thanks to iCloud. The new Mac client is out now.

MetaMoJi Note, previously Note Anytime, is a powerful notetaker, PDF annotation tool, and a digital scrapbook for your life. Capture your ideas anytime with advanced handwriting recognition and handwriting to text conversion, or annotate Office and PDF documents. Use the app as a high resolution sketchbook with a vast color wheel palette, pastel colors and advanced calligraphy pens. MetaMoJi Note is a virtual whiteboard for sketching, annotation, scrapbooking or digital mashup.