How do you decide which links should be placed in the primary menu? Should you only link to the pages and areas that get the most traffic? How should you think?
How do you decide which links should be placed in the primary menu?
I'm not going to get into the complexity of how to consider and structure your global, local and other navigation systems (although see Card Sorting on boxesandarrows) but the first consideration is to think about how your target audience will use the site. In fact even before that, you should consider the question:
Do I have more than one target audience?
Is the scope of appeal such that I may have a variety of different audience types who are interested in sets of destination pages which have little or no overlap. For example buyers and sellers; publishers and advertisers; domestic and business. This is indexing for specific audiences, but don't ignore the possibility of having a unified indexing system to cover all audiences, or even whether you should create more than one site.
Do I have multiple topics?
If my content is such that there are clearly identifiable topics, it makes sense to organise by those topics at the top level. This is only appropriate if you have a manageable number of topics, otherwise you should find a way of grouping content in a more digestible manner. Since topics are less likely to overlap, their organisation should be alphabetical or similar so as to aid quicker scanning.
Do I have recent content
If my content has historical or chronological importance then make that the top level organisational structure so that visitors can see what's new, what's changed or what's current. But be sure to always have something current as that's likely why visitors will return.
To be honest, if you know your user, and you know your content, the primary navigation system should seem to fall into place. If you can't connect the dots between what your users are looking for and the structure of your website, then something went wrong between concept and creation.
Should you only link to the pages and areas that get the most traffic?
Well that's not really answerable without knowing whether those pages fit into any of the above considerations - or any other pattern that best describes your site (The above list of consideration is general and incomplete). Nor is it answerable without knowing why those pages are already getting the most traffic. Are they getting the most traffic because they are useful to your audience and being found or are they getting the most traffic because they already have prominence on the website, or because they are appearing high up in google search results and being used as a landing page. I would consider the whys of the current situation as well as what you would do if the site wasn't even public yet.
How should you think?
You should think like your users.
The information architecture project design stage of the site is where the site sections would be identified. Ideally using card sorting (or other methods involving discussions with the potential users) which will provide you with a potential logical structure for the site, what pages should be grouped together, what belongs where, and what content isn't actually required at all.
Planning, talking to the users and grouping the site content logically will help you identify what to include in the primary navigation. Get the content sorted first and then work out where everything belongs.
There is a great article on Smashing Magazine about setting out your navigation: Planning And Implementing Website Navigation