I think the most important keywords are the ones the search engines are showing me for. At a minimum I want to track the rankings. I usually still have some keyword I am developing ranking for, some choice ones I feel will convert well, however the terms sending traffic and getting shown are really the most important.
I take the keywords shown in Google Webmaster and in Google Analytics then run them in a Rank Checker. To me these are the real world keywords because they are bringing traffic or seen and shown by Google.
Getting the list of words from Webmaster is just a matter of exporting the list. To get the words from Analytics I have to copy the whole data set shown in my Google page then paste that into Excel as “Paste Special” text; then I can copy just the list of words.
I like the Traffic Travis Rank Checker because it is fast and when I paste in an updated list of words it automatically adds the new ones without duplicating any. You can get a free copy of Traffic Travis - click here . SEOBook has a good free Rank Checked Tool here.