Hello,
One of the tools that I have used for back links is called SEO Spyglass a program that's part of the SEO Powersuite. The program is pretty accurate and offers unlimited use but can be slow at times.
Moz Pro also offers a variety of great tools like Open Site Explorer that allows you to retrieve and view back link data. The results were near identical to SEO Spyglass but Moz allows for instant results versus waiting for two hours of software running in the background.
I have also heard of Raven tools and Majestic SEO but have not used those tools personally.
Using any of these tools, you can export the acquired data into an xml file or excel file and then manage your back links using any spreadsheet software.
I personally use Microsoft Office 2013 but may also choose to use tools like Numbers for Mac, Google Spreadsheet, or open office.
Hope this helps.
