Scanbot - Scanbot is a mobile app that allows you to use your device's camera as a document scanner. The app is capable of scanning a large number of source materials, and it can handle QR codes as well.

Mendeley - Easily organize your papers, read & annotate your PDFs, collaborate in private or open groups, and securely access your research from everywhere.

Scanner Pro - Scanner Pro turns your iPhone into portable scanner in your pocket.

Zotero - Zotero is a free, easy-to-use tool to help you collect, organize, cite, and share research.

Genius Scan - On The Go.

Qiqqa - Qiqqa is a free research and reference management software. It can be used in many organizational projects from the academic to the personal to the business endeavor. Read more about Qiqqa.