As it happens MrFewkes I've recently been playing around with that same tool (I'm guessing we all know which one it is) and I found a few interesting things that are worth bearing in mind. Just personal opinion I got from playing with the data in Excel but I thought you might find it interesting.
First off, like Tedster said, you've really got to look at linking domains and not at raw link volumes - it can tell a totally different story .
Secondly I found that the tool seems to have followed links from Google Display Network or Adsense or something because I found a period (08-09) where my site's aquired links shot up with links from MFA sites (no we hadn't been buying links).
Thirdly I noticed that using article marketing you can get content syndicated onto 500 new domains a month but I know from personal experience that although this does creates a big spike it doesn't actually move the needle when it comes to improving rankings (please feel free to correct me if I'm wrong on this one). So I started thinking that if Google applies a filter to some links it might be worth trying to do something similar with this data so I stripped out links from low quality pages (using that tools quality metrics I removed anything with a score of less than 3) and it totally changed my appreciation of the data.
Fourthly I used a SEARCH function in Excel to determine whether the anchor text of a link was branded or not (whether it contained the site's brand name). Plotting the aquisition of branded and none branded anchor text next to each other was amazing. In some cases you could see where sites had hired their SEOs just because the pattern changed so much. Unfortunately before I could run an analysis on some sites with statistically significant link profiles (i.e. national brands) my monthly download allowance using that tool ran out.