If you have small numbers of nav links, you can put them on the top.
For example, this ux.stackexchange forum.
If you have a lot of nav links, you can categorize them to shortlist the number of immediate nav links and still put them on the top. For example, Amazon User's Menu Area
If the number is still big, you can put them on the left, like the typical CMS admin page that you have seen.
The strategy really depends on the content of your site.
Big sites like Amazon will adopt a mixed strategy.
You can try several approaches and do usability testings to figure out which one works best for your case.