Research (find) the most relevant Words and Phrases:
In order to optimize the keywords of your website, this is the first-most step, find loads of theme relavant words and phrases which are deeply rooted into the core content of your website. These are the keywords most likely people search in google, yahoo, msn live etc. After finding, refine this keyword list you have come up with. Then you should sort this list by popularity.
First place to begin your research would be Google Adwords, as far as I know nothing beats this tool.
Which pages to begin with?
The next important thing would be, which pages to focus on? I would use Google webmaster tools over here.
These are the pages that are linked to, this also explains how the internet out there is linking to you. How about pushing these pages to higher level? Research keywords found on these pages and share them on social sites.
Before we go any futher, I would like to caution, don’t ever stuff your website content with these keywords in a crazy manner. The whole theme and content as well as latent semantic environment of your site should revolve around these keywords. Crawlers and Robots can easily differentiate between content generated by scripts / automated programs and real human beings.
The Basic Technical Part
Now is the time to use these refined, researched again and again keywords into your website. First step would be to insert these into your Title, then into your description meta tag. After this use these keywords in the header part of each page.
Write Content and Articles on these Keywords
Now write huge loads of content and articles on these keywords, don’t hesitate at all. Educate people on these keywords, how to use them, how to root them in your website.