Website Design for Theme Based Search Engine Indexing
When a theme based search engine spider crawls a website, it reads it in the following manner:

Domain Name - countdowntoarmageddon.com
Sub Directories - Iraq war, prophesy, earth changes and survival
Page Title Tags - Learn more about page title tags and seo
Meta Tag Data - Learn more about meta tags and optimization
Headings. <H1> <H2> - Learn more about header text and optimization
Outgoing Links - Anchor text, attributes and surrounding text
ALT and Title Attributes - Learn more about alt and title attributes and seo
Named Anchors - Hyperlinks to help navigate your website
Body Content - Main body of content intended for visitor
Once the search engine spider has finished reading the text it does the following:

Delete all filler or stop words - These are words like and, or, the, web.
Identify recurring keywords - Words recurring throughout the site.
Stem the identified keywords - Survival becomes survivor, survivors and surviving.
Identify keyword phrases - Survival becomes 'survival gear'.
Weight keywords using common indexing methods - Proximity and density for example.
Establish the websites theme, based on the dominance of keyword and keyword phrases.
It may sound simple enough, just keep every area of a web page rich with keywords. Unfortunately, it isn't that simple when you have a website as diverse in the eyes of the spider as countdowntoarmageddon.com or worse yet, a department store website selling everything from perfume to lawn mowers.

A search engine using theme based indexing technology gets confused because the website appears to be diluted with unrelated information. It can't decide if the website is about survival, the Iraq war, earth changes or prophecy. As a result, the theme based search engine will interpret countdowntoarmageddon.com as less relevant for all the above queries.

The question now, is what to do about it?

Identify your Website Themes
Your Website's theme, or search engine theme, is simply what your website is really all about. Strip away any slightly off topic pages. Forget about the obscure, far reaching terms you may have considered optimizing for in an effort to grab as much peripheral traffic as possible. Then ask yourself... "In as few a words and phrases as possible, what is my website really all about?"

If your website is about several different things that a theme based search engine is going to interpret as unrelated, then you may want to consider dividing your website into as many different domains as you have unrelated themes.

In addition, it's always best to have each domain hosted on different servers with different C block IP addresses, and then cross link between the different websites any and all content that is related.

Learn more about Cross Linking and the importance of splitting up your website into as many different separate domains as you have unrelated themes by readingf The Power of Cross-Linking.

Designing a Website for Theme Based Search Engine Indexing
Select a keyword intense domain name using hyphens.
Name all sub-directories with keyword names using hyphens.
Include your most important keywords being optimized for in web page titles.
Deliver consistent keyword meta tag data, unique for each page, throughout the website.
Use header text to deliver consistent theme information throughout the website.
Assign keyword relevant contextual text links.
Use ALT text on all graphics and graphics links.
Use Title attributes on lists, forms, section headings, images, hyperlinks etc.
Link liberally to authority websites which are relevant to your theme.
Riddle body text with keyword phrase intense information using synonyms and stemming.
Ask other on topic websites, hubs and authorities to link back to you using keyword relevant links, attributes and surrounding descriptive text.
In order to create a good theme based website you must be consistent, which is easy when building a website from scratch, not so easy for some existing websites.