Collar the Spiders
You can collar and attach a lead to search engine spiders and make sure that they don't stray away from your web pages too soon, particularly your home page that is liable to receive the highest search engine listings.
Spiders work from top left to bottom right, and if you have tables on your site, they start with the top left table, and scan its contents first, then go the next table and so on. If your website is designed using tables rather than CSS, and you have a left hand navigation table and then a table containing the bulk of your content, the spider will read your top navigation link first, and leave your home page. It will not return until it hits the home page link.
It will therefore miss most of your content. The answer is either to place your navigation table to the left of your content, so it is visited after your content, or to use an empty table top left, then a content table, then a left aligned navigation table. That way the spider will visit the empty table, then your content and then your navigation table, which is still showing to the left of your content, but comes after it in your HTML.
You then receive the full benefit of your great keyword and semantically optimized content, rather than waste it by the spiders looking elsewhere for your main content. When relevance to a search term is calculated, (keyword), spiders give most weight to what is contained within your H heading tags, the first 100 or so characters in the body of the text, and your final paragraph. Your Title Tag is also very important, and you could put your company name and the main keywords there. That helps your branding and the calculation of your listing from the keyword.
Internal Linking Strategy
Now that you know where your links to appear to spiders, where should they point to? If your site is silo structured, then your home page should link to each of the main silos. Do not link to every page in your website, but to Level 2 pages that provide further links to your level 3 pages. That is because but Google's Page Rank is calculated on internal links as well as external links. Only link your Home Page to every other page if you want the maximum possible share of your site PR for your Home Page.
Your total site Page Rank is equal to 1 vote for every page on your site. So if you have 20 pages, you have a 20 PR votes to distribute. That does not mean that you have a Google PageRank of 20 - far from it. Nobody but Google know how many links or PageRank points/votes are needed for each Page Rank vote. It could be 10 for a PR of 1, 100 for 2, 1000 for 3 and so on, or something completely different.
The internal Page Rank for each page in your site can be calculated since it is a function of both the page rank of pages it is linked to and the number of other links leaving that page. You can use this to maximize the PR votes for any page on your site, or spread them around pages you want listed highest. This calculation involves both internal links and external links.
In fact, you can make an appreciable difference to your SEO and Page Rank if you use a sensible internal linking strategy. With a 10 page website, if every page is linked to every other page, then your internal PR votes are one for every page. However, if you link Page A to page B and then Page B to every other page, and all pages back to Page A, you can give Page A 3.42 PR votes, page B 3.06 and the rest 0.44, thus optimizing the PR of your first two pages (note how these figures add up to 10: 1 for each page).
If you want to give your Home Page maximum votes, link it to every page in your site, and every page back only to the Home Page. For the same 10 page site, Page A then gets 4.67 Pr votes, and the rest 0.59.
However, for a silo site, it is best to have the main silo pages with a reasonable share of the votes, so link the Home Page to the main silos, and then each main silo to the sub-pages in their silo. Everything links back to A. This gives your Home Page 3.60 and your silo pages 1.17, the rest 0.40. There are several options in between these, but the point is that you can use linking strategy to maximise the PR for any page on your site.
No Follow: Beat the Spiders
The nofollow attribute was devise by Matt Cutts of Google. Its intention is to enable you to link to a page without giving that page a share of your PR. This can be used when you are linking to pages that have no outbound links, and for which a PR would not be meaningful. Google claim that it uses the term literally and does not follow the link at all, but test results have been conflicting, and it appears to follow it, but not index it.
Different search engines interpret 'nofollow' differently: Yahoo do not include pages linked by use of the attribute in their rankings but does follow it, MSN does not count links with 'nofollow' in their ranking and Ask ignores the attribute and follows everything!
It therefore appears that you can use the attribute to prevent spiders from leaving your site by following every link. From my own experience, I seem to get few spider visits to pages attainable by means of a 'nofollow' link, and so can use this to prevent spiders going where I want them to go.
Advanced SEO techniques can be used to lead search engine spiders where you want them, and prevent them from being sidetracked by poorly positioned links to other pages on your site. You can use your internal linking strategy to optimize the Page Rang votes for each page in website, and can also prevent some pages receiving a share of your sites page rank.
It is important that Google should be able to spider or list all of your pages, since that can not only dilute your overall PageRank but affect your listing position, but if you have too may low value pages being navigated and indexed by search engines, they may put you on a reduced crawling status. Try not to have lower value pages put on a crawling par with your higher value pages that you want listed higher in the SERPS.
This is just an introduction, and if you visit SEOcious you will find more details of how to calculate your own internal Page Rank points, and how to use various techniques to control how search engine spiders crawl your website.