I use the ForScore iOS app to store all my PDF scans in iCloud. Mark-up is done in the app using an digital pencil (Apple or Logitech) on an iPad. ForScore has scan-to-pdf feature that eliminates the hassle of importing a file. It's also got the ability to share locally with other app users via Bluetooth. Also works with Bluetooth page turner/ MIDI pedals. It is a feature-rich application with a very intuitive user interface, so getting up and running is pretty quick and easy. The downside is the cost of the tablet and pencil, and more if you add a stand and a tablet holder, but when you look at all the tools that a iPad adds to the pocket of your gig bag, it's pretty much an essential piece of gear.
