As someone who has done work for many many many clients across the engines for a long time now I can honestly say that keyword density never has, and never will (unless things seriously change) figure into any of the work I do for my clients. You can analyze the top results 'till the end of time but you will never see a real trend. The one and only thing to focus on is the use of English on the page, what do I mean by that? Well you probably hear many people calling it copy, and they are right. Get the words on the page, in the tags - structured the right way and away you go. Dont ever ever worry about density...trust me...ill make you a superstar!
doesn't really matter how you do it IMO - just make sure you use a uniform approach - if you include stop words then always analyze including stop words or vice versa - that said I'd do it with out stop words.