Personally I love using includes and requires to construct your page.
The part where you draw the line is including everything.
Let's say I have a web app that let's people resize photos online, on the homepage I would include the header, a sidebar, the homepage content area, and a footer.
The main part to focus on here is the homepage content area, if they were on the homepage there would be no point to include or require the file that handles the functions for resizing images.
If you would like a real world example of includes and requires and how effective they are, check out any Wordpress blog. I have a few clients that have wanted to use Wordpress as a CMS and to this day they still function superbly even with tons of data and user flowing through them.
Also, this subject has been covered multiple times, feel free to check out: http://stackoverflow.com/questions/786929/one-large-include-file-or-several-smaller-ones
Hope this helps.