Over the years I've had many iterations of websites, each time feeling that either something was wrong or something code be done better. I've swayed between the simplicity of WordPress, and coding from the ground up. Eventually I've ended here with the latter. WordPress has always left me feeling that I could do a certain aspect of my website better, probably because I don't need the power of a full CMS, and would much rather have the flexibility provided by building from the ground up.
The structure of this site pretty much resembles that of a static HTML website, but with a bit of PHP thrown in to avoid to much repetition. Each page is represented by its own PHP file, from there I determine the relevant page elements to include (navigation, comments area, CSS etc.).
Whilst this means that I have to manually create a new file for each new page, and maintain all of the links myself I actually see it as a benefit - it means I know exactly where everything is, and since everything is file based can easily be stored within a Git repository.
This site (along with many others) is hosted on a Linode VPS.