iAnnotate (US$9.99) is a full-featured iPad app for marking up PDF files with highlighting, diagrams, notes, and even audio comments.
Standout features include the ability to markup DOC and PPT files as well as PDF documents. The app allows you to have eight documents open at once, something many of its competitors don't offer.
There is a broad arrange of annotation tools, and you can create custom toolbars to speed your work along. For importing you can use Box, Dropbox, Google Drive, Microsoft OneDrive or WebDav, plus iTunes file sharing is supported. The app doesn't support iCloud, which is a negative, but Air Drop is supported. You can also open emailed PDFs.
Documents can be searched quickly, and you can create folders to keep projects in a workable environment.
I gave the app a try and found it easy to use, although extensive help is included if you need it. Drawing was easy, and you can choose a pen, line tools, underlining, and time and date stamps. There is a keyboard that is used to type notes in different colors than the document. Copy and paste is supported between documents. All the functions worked well, and sharing of the annotated documents was easy through email. I tested opening my documents in Adobe Reader and Apple Preview under Yosemite with no issues.
This is a powerful and useful app if you find yourself needing to mark up documents for sharing and circulation. The variety of tools and customization is a real plus. As mentioned, iAnnotate PDF really needs to add iCloud support as it will be the default sharing method for many iOS users.
iAnnotate PDF requires iOS 6.0. It ran nicely on my older iPad 2, so just about any iPad that can run iOS 6 or later will be fine.
Other similar apps that are well thought of include PDF Expert 5 ($9.99), PDF Forms (which I reviewed last month - $8.99) and PDF Pro (free), which has a reduced feature set compared to the others.