Spiders can't see links that are accomplished by Javascript so, as far as search engines are concerned, they don't exist. Don't use them if you want spiders to follow your links.

Google won't spider any URL that looks like it has a Session ID in it, so URLs with longish numbers in them must be avoided. These are usually dynamic URLs.

Make sure that all pages link to at least one other page. Links to pages that don't link out are called "dangling links", and the reason to avoid them can be found here.

It is good to structure the internal links so that targeted search terms are reinforced. E.g. organize the links so that a topic's sub-topic pages link to the topic page with the right link text (see below), and vice-versa.

Off-page elements

Link text
<a href="url">some link text</a>
This is one of the two most important elements for good rankings. The link text can be on pages within the site or on other sites' pages. Either way, it is important. The target page's main search term should be included in the link text. When possible, don't use identical link text for every link that links to a page, but do include the target page's main search term in the link text.

Google attributes link text to the target page - as actually being on the target page, and it treats it's pseudo-presence as being an important element of the target page. Links carry even more weight if the text around them is concerned with the target page's topic and search term(s).

On-page elements

The Title tag
<title>some title words</title>
This is second of the two most important elements for good rankings. Make sure that the page's search term is contained in this tag, and place it as near to the front as is reasonable, whilst ensuring that it reads well. There's nothing wrong with placing the search term up front on its own, followed by a period; e.g. "Pagerank. Google's PageRank and how to make the most of it". The target search term is, of course, "PageRank". Obviously each page's Title tag should be different to the Title tags on the site's other pages.

The Description tag
<meta name="description" content="a nice description">
Some search engines, such as Google, don't display the Description like they used to do but, even so, it should still be included in each page for those engines that do, and for the odd times when even Google displays it. Write an appealing description for the page and incorporate the page's search term into it at least once and, preferably, twice. Place one instance of it at the start or as near to the start as is reasonably possible.

The Keywords tag
<meta name="keywords" content="some keywords">
The words in the Keywords tag were never treated as keywords by the search engines; they were treated as text on the page. The tag isn't as effective as it used to be but there is no reason to leave it out. So put plenty of relevant keywords into the tag and include the search term once at the front, and a second time further along the line. There is no need to seperate keywords and keyphrases with commas, as is often done, since the engines ignore commas.

The H tag
<Hn>some heading words</Hn>
"n" is a number from 1 to 6; the biggest heading size being 1. H tags are given more weight than ordinary text and, the bigger the H size, the more weight it receives. So include the target search term in H tags at least once on the page, and two or three times if possible. Also, place the first H tag as near to the top of the page as possible.

Bold text
Bold text is given more weight than ordinary text but not as much as H tags. As much as is reasonable, enclose the search term in bold tags when it appears on the page.

Text
Use the search term as often as you can on the page whilst not detracting from the page's readability. Make sure that you use the term once or twice very early in the page's body text and as often as possible throughout. Reword small parts, and even add sentences, to make sure that the search term is well represented in the text.

In all probability, each word in the search term will be found on the page seperate from the search term itself. This is good. In fact, if they are not there on their own, add a few of them through the page.

Alt text
<img src="url" alt="some alt text which is displayed on mouseover">
Include the search term in the alt text of all images on the page. Keep in mind that some systems such as Braille readers and speach synthesisers use the alt text, so you might want to make them usable whilst including the search term.

Summary

1. Select your main search terms.

2. Allocate each search term to a suitable existing page. Split some pages if necessary.

3. Organize the internal linkages and link text to suit the target search terms and their pages.

4. If possible, organize links from other sites to suit the target search terms and their pages.

5. Organize all the on-page elements to suit each page's target search term.

6. Sit back and watch your rankings improve!