Andre Scholten, a Dutch SEO, wrote a great post (in Dutch) about SEO tracking / SEO Analytics. It's an interesting idea to track SEO efforts with Google Analytics and the way it can be setup, is done really smart. Yoast, one of the most famous Wordpress-SEO gurus, allowed Andre to re-post it on his blog (in english) and it draw quite some interest.
The post is very detailed and written very well, however I miss the part where some warnings should have been posted. If a user installs Google Analytics, they have to be aware of what they are getting into. I am a big fan of G Analytics and I don't want to go in details, but some sites should stay away of tracking their linkbuilding / SEO efforts with a tool from a company that also runs a search engine, a toolbar, an ad network, an email business ... .
It's not about being paranoid, but there should also be caution when it comes to free tools, even if they have a big Google logo on top of it.
Same also is the case for other G tools like Adwords. I for myself will never run an Adwords campaign on a not 100% ready site again. And I know why :)