Before you actually start filling your site with content, decide upon a logical structure for your site. First of all, this will make it easier to build your site, especially for larger sites. Also it can prevent you from having to re-structure your site later on. I often perform SEO audits and while many issues are easy to solve, this one is not: Restructuring a website often leads to changes in the existing URL's of your website, which could have negative impact in the search engines. Of course you can correct this with redirects, but it creates additional work that you can avoid by starting off right.
By carefully creating a logical category structure both people and search engines will find it easier to understand your site structure, and it also helps to maintain the site. What can often help is to make sure the category structure and the menu-structure are set up in a similar way. On Joomlaseo.com, I have categories for SEO-checklist, Performance, Extensions, Audit Tools and Blog, and you can easily see that this is exactly how I have set up my menu.
What also helps for SEO is to link back from any article or subcategory to the category level above (using breadcrumbs, or by setting the Show Category option in the article settings). If you also fill the category-page with useful content, they receive more authority. This is why I usually try to prevent having categories without a description. Just check out the main Checklist page on this site. It is not an article, but a category page, and all articles in this category link back to it. If you do this correctly, your site will have a pyramid-like structure, with the home page on top, main category / menu next and individual articles at the bottom:
In the SEO world, we often speak about link-juice. This sounds a bit magical, but we use it to indicate the flow of links to certain parts within a website. Pages receiving many internal links are relatively strong (also read this excellent article about silo-ing your URL-structure). Because the pages higher up in the pyramid automatically receive a lot of link-juice, they are seen as pages with a lot of importance, which might make them stand out. This makes them suited for competing for competitive keywords, while the pages low in the pyramid, typically your individual articles, are more suited for targeting so-called long-tail keywords (low traffic, but very relevant). In some cases, this even can even result in perfect sitelinks in the Google SERP, displaying your main navigation.:
If you take this technique even up one level, you can use it to create so-called SEO-silos in your website. To learn more about this, read this (non-Joomla) blogpost by Authorityhacker.com or this one www.alfredlua.com/seo-topic-clusters.
Avoid going to deep with your URL structure. You should not go further than 2 levels deep. Going deeper then this is first of all confusing for users, but also makes the purpose of the site less visible for search engines. Some examples:
Of course, there may be exceptions where this is hard to achieve, like large webshops or product catalogues.
As well as avoiding deep link structures, you should limit the number of items per menu. Users often get confused or bored when more then 7 menu items are visible in a menu, and confused users often leave the site (=increased bounce-rate = bad SEO rankings). Instead of stuffing all your menu-items in one menu, you should either use sub-menu's, or fly-out menu's (make sure they work on mobile devices).
Joomla creates URL's based on the menu-structure. If the article is not accessible through a menu-link, the URL will be based on the Category - Article structure. The actual URL is based on the alias of the Menu-item / Category / Article. So, a URL is usually created for every menu-item, even if 2 menu-items link to the same article (avoid this, it leads to duplicate content issues). The topic about URL's is actually pretty extensive, and it goes a bit too far to go to deep here. My Joomla SEO book covers this in much more detail.
My advice is to always make sure every piece of content is linked to a menu-item. If this is a single article item of a category blog collection does not matter, both are fine. If you do not provide for a menu-link, you may even end up with content that cannot even be reached by users: orphan pages.
One last tip here is to make sure you build a menu-structure that you oversee. If possible, only use one menu.... This is easy enough to arrange.
Joomlaseo.com is fully built and written by Simon Kloostra, SEO Specialist and Webdesigner from the Netherlands. I have also published the Joomla 3 SEO & Performance SEO book. Next to that I also sometimes blog for companies like OStraining, TemplateMonster, SEMrush and others. On the monthly Joomla Community Magazine I have also published a few articles.