I have Media2D and Media3D folders, you can split up the media more if you like but this way makes creating the installer a little easier.
I have also recently stopped having my include/source files in my project folder. The main reason is that its easy to backup all your code files in one seperate folder rather than saving the project which contains Debug/Release folders and intelisense file which can be huge when you add it all up. You can clean the solution but I often forget and usually have multiple projects per solution. Also, when you make your release you dont need all the code files anyway.
Just do what makes sense to you, there are so many different methods, also depends on the size of the project alot of the time.