There is an excellent thread at HighRankings Forum on the topic of how you should or could track one's link building efforts. The topic in this thread started off about how to track links accrued due to a link building contest. However, the topic moved into how to track link building efforts for a site in general.
Many are of the opinion that no tool can accurately measure the links acquired over time. Google Webmaster Tools, Yahoo Site Explorer and the various other tools, to many, are not that accurate. As Rosemary said in the thread, "one month Yahoo would show 10,000 inbound links and the next month only 300." It is hard to rely on tools that you don't know how it works and when there is a bug, you cannot fix it yourself.
Others say that when they build links, they store the information in a spreadsheet to report back to the client. I have seen this done. I am a firm believer that if you are hiring a link building company, they should provide you with an organized means of knowing what links they acquired for you, from where and when they acquired them. I have said this before, so I say it again.
Others in the thread said they just gave up on collecting and monitoring this data.
How do you track your back links?
Forum discussion at HighRankings Forum.