The content keyword list in Google Webmaster Tools measures which keywords are used on the most pages on your site compared to other sites. So if you have a shopping cart on every page of your site, you will have "cart" in your content keywords. Words like "the" don't show up in the list because most sites have them on every page.
As long as this list doesn't have spam words on it, it isn't hurting you. Google says that you should watch this list to see if your site is hacked. If you see "viagra" on this list, then you know there is a problem.
The words on this list don't indicate what you are likely to rank for. Google's relevance algorithms are much more sophisticated than "used on many pages of your site." The relevance algorithms take into account:
- If the word is used in the title
- If the word is used near the beginning of the title
- If the word appears in headings
- If the word appears multiple times on the page
- If the word is used in inbound anchor text
- If users click on your site Google puts it in the search results for that term
The "content keywords" don't appear to factor in any of these other relevancy factors, just how many pages on your site use the words.
I've tried adjusting the words on my site to make this content keywords list more accurately reflect the thing I would like the site to rank for. In my experience, doing so doesn't help. Using a word on more pages on my site doesn't seem to help my rank better for those keywords. Removing irrelevant keywords doesn't make the remaining keywords rank better.
Bottom line: don't worry about the content keywords unless there is spam listed.