Where to keep PHP pages for iframes??

One site (5) in my multisite community has a lot of custom code, forms, reports, etc., which are built as PHP pages. I'll include these pages inside WP with an iframe.

My question. . . where should I actually put these PHP pages?? Special folder off the webroot? In the theme folder? Other?

I would like to keep them somewhere that I can later see that they are related to site 5. What's the best practice here?