difference between linux distributions using Gnome
 

Just wondering,

What is the difference between using Gnome Desktop Environment on one linux distribution and using it on another. Except from how they boot, and the hardware they asupport etc.

Some distributions include extra scripts / GUIs for tools that make your configuration easier than others. Plus, the distribution of files in different folders is slightly different in every distribution (not a big variation but important if you want to know your system by heart)

You said some files are stored in different folders.

Also, are the folders differently arranged? and are some folders named differently?

Example, will the /etc/ folder always be called that in every distribution? or will some distributions call it something different?

No. that shall forever be that :) These directories like /src, /mnt etc. are part of the linux file structure and are always known by these names