TheMadScientist - 7:46 am on Jan 22, 2013 (gmt 0)
Oh, if I'm reading your post you were making at the same time I was making mine right and the links are on your site, then I'd definitely run them through a redirect, store the info and strip the query string before the visitor landed on the destination page ... No question for me, there's no way I'd go with 'ugly URLs' for onsite visitor tracking ... Check out what happens here when you click a link that's posted rather than hard coded into the HTML (except links to posts) ... They all run through a redirect.
Here's an example...
Hover over it and see where it actually goes.