maybe like in mysite/code/feature/templates/Layout?
oh. umm… either in the theme or in mysite/templates
those will be global 🙂
the only issue would be if you were overriding templates also used by the cms. If thats the case - they should go in theme
@adrexia I had a recent run-in with that issue. Overriding Forms and Field templates is a perfect example
unless you want to override cms templates 🙂