One of my favorite, easy-to-use features in Linkscape is the ability to compare pages and domains side-by-side to see which ones have earned what relative quantities of links. For example, I was curious to see how people linked to SEOmoz (since we're on a .org and I see lots of links to .com). Linkscape to the rescue:

Obviously, www.seomoz.org is the most linked-to and highest mozRank of the pages, but it's fascinating to see what percentage of folks link to seomoz.org (with no www) and to www.seomoz.com (which, thankfully, we own and redirect). I can then take a look at some more interesting data in the advanced report, specifically the number of unique domains pointing links at those different sites:

(BTW - see how 7.79 is only 11.99% of 8.82? Crazy, but that's how the logarithmic scale works. Good to think about next time you're comparing mozRank or PageRank for URLs or domains)

We'd be losing out on quite a bit of external link juice if we didn't own/redirect these domains properly. Furthermore, seeing those stats on the number of unique domains that actually sent the links is utterly fascinating (and something we've never had access to before). I think domain diversity of links is a phenomenal stat just on its own.

There's another key application here that I've been leveraging on some client campaigns of late - the ability to check out multiple pages for a single domain and better judge how to use them for keyword targeting. I'll walk through the process I use:

Step 1 - Run a query at Google for the keyword phrase + the site. For this example, I'll use link building site:seomoz.org. I can take that list of links and go to step 2...

Step 2 - Plug them into Linkscape's Comparison:

Step 3: Smack Self on Head - Seriously, it's like I've got dumb written all over me. Of course most external links point to the link building guide (an updated version is set to be re-released in the next 3 weeks, BTW!), and of course no one links to the blog category! If I had any brains at all, I would get my internal links (and all the mR I've built up there) lining up with my external links and point them at the link building guide. I'll bet I could get some much better rankings for the search phrase link building in the engines and probably drive a lot more high value traffic.

Now obviously, this won't always be so simple to implement. For us, it's just a matter of adding more internal links to the guide and maybe changing the name of the blog category so we're not keyword cannibalizing. For your site, it might be a more involved process. Nonetheless, the power of comparing reliable, trustworthy link data is immense. I'm not at liberty to show the client site we recently used this on, but I know they're getting a lot of really high value, high converting traffic thanks to the data uncovered.

BTW - I don't want to make it out that Linkscape is the only way to do this. Technically, you can do some of these processes (minus a few of the metrics and the domain diversity stuff) using advanced link queries at Yahoo!.