Currently, I'm trying to organize all of my game development code (such as it is) as sub-projects in Visual Studio, with a single location for external libraries (SDL2, Lua, etc.) and a single repo pushed to Bitbucket. Visual Studio doesn't seem designed for that, so it's awkward, but it works.
And for web development, Just a separate folder for each project and XAMPP. I'm a dinosaur and never even started working with a VM until recently, so I've got one Hack project running in Vagrant, but I still prefer XAMPP.
Other than that, I don't impose a lot of structure on my projects because my side projects are more about education and exploration than trying to come up with a MVP or resume filler (although I'd probably be in a better position if I thought more about the latter than the former.) Just enough structure to make it easy to start and archive, then as much anarchy as I want.