Don't be afraid of lots of little files.
Group your functions into conceptual chunks - if you've got several functions that routinely call each other, for example, group them into the one file. If you often find yourself using the same functions in combination with each other, group them together. Make function libraries, in other words. If the functions in a library turn out to be really intimately associated with each other, consider wrapping them in a class.
Then just include the ones you need. If you find some of your libraries including other libraries, then for safety you should use include_once() instead of include() - that will stop PHP trying to include something it has already included.
If you've got functions relying on global variables (except those PHP itself provides) ... well, the short answer is, don't.