The only other links on your homepage are likely to be links to important sales pages on your site – the "money-makers".
I usually keep most of these in a side menu, and update them using server side includes (SSI). If you don't know how to use SSI, you should learn (a gift I am giving you next week will include a primer on SSI).
It is also good practice to include links to important pages from within the body of your text. This type of natural linking is expected by the search engines.
One thing to avoid is linking to other sites from your homepage using standard links. If you want to point your visitors in the direction of another site, I recommend you do it dynamically (with the exception of link partner links on your links page).
That is a summary of the linking from your homepage (I hope I have not forgotten anything).
The next stage is to think about linking from the other pages of your site.
Since incoming links to a page are so important to a page ranking, this is very important. The problem here, is that as your site grows, it is very difficult to get enough links to each page.
If you have followed this course so far, each page on your site will have links back to the homepage, which is good. However, each page of your site will eventually have PR, and should therefore be used to do some work. Use links on all pages of your site to link to the important pages of your site. This is easily done by using a menu (similar, if not the same as the one on your homepage) on all pages. As your site grows, links to each important page increases, and so will its ranking (this is one of the reasons adding lots of content to a site is a good thing – it helps important pages on your site rank better).
If you have followed this linking guide so far, then there is one problem. That is your article pages. How many links will each article have pointing at them?
The answer is only one – the one from the article map.
This is not enough to get an article to rank well, so I like to use my article pages to link to other, related articles. If each article had links to five other related articles, then each article will quickly build up incoming links, and that in turn will help each article rank better.
The other thing I like to do is to get incoming links to my important article pages, and even the article map. This boosts the PR on the article pages, and since my articles are cross-linked (which is OK when the cross-linking is on a single site), all articles ultimately benefit. An easy way to do this, is to link to articles on your site from within the articles you submit to directories. If the article directory does not accept internal article links, then use the resource box for this purpose.
The simple rule I follow is this:
If I want a page to rank better, I get links to it (and/or add more links to it from within the site).
That is nothing new, but many webmasters forget about their articles, and wonder why those articles don't rank so well.