Picking keywords to target with SEO efforts is much more complicated than it looks. Many variables should be taken in consideration when choosing keywords to keep track of SEO success.
One distinction I would like to make is for small websites, the SEO keyword list should be all inclusive. On small websites, with under 100 Web pages, each page of the website should be mapped to an individual keyword. Large websites, with over 300 Web pages, should pick keywords to report on that best represent different sections of the website. Each URL should still be mapped to one keyword but you will only report on under 300 keywords (any more can be un-manageable).
When creating your SEO keyword list:
1) Theme Relevance - Create a list of URLs and their corresponding keyword theme. Make sure to include a keyword that is relevant to current content. You can also add keywords to the SEO keyword list that you plan on optimizing for in the future.
2) Google Impression Share - You want to make sure that the keywords you add to the list have some Google impressions. However, don't get trapped in the selection of very generic keywords just because they have a lot of impressions. Consider the following variables to refine your keyword list, after impression share is identified.
3) Competitiveness - The keywords you choose must allow you to rank in the top 5 rankings. See who ranks in the top positions, are they websites that own the top spot or can you break into the top 5 spots. The majority of Google users will only look at the organic search results above the fold (make sure you can get ranked here).
4) Revenue Generation - There is no reason for you to try and rank on a keyword that doesn't offer revenue (or the goal you are trying to receive). I have ranked in Position 1 for very generic keywords that have a lot of impressions, however we didn't get any conversions. You want quality as well as quantity.
The difference between SEO & PPC keyword list creation is with SEO you want to map one keyword per URL. Whereas, with PPC, the goal is to exhaust the different combinations of keywords that your customers would use to search for your website. Same idea but a different strategy.
Don't forget to revisit those SEO keywords every 6 months, you may find that the keywords you thought would work don't.