PHP Objects, Patterns, and Practice

I'd personally reccomend PHP Objects, Patterns and Practice

Disk is a slowest part of the server, so in this case variant "all functions in 1 file" will give you little more performance, theoretically.

But I don't recommend you to create "functions.php", better way is OOP. Create classes (objects) with methods, use autoloaders and PSR-0 standard and you will forget about "include" and "require" at all.

Thoughts:

1. While exists at least 1 way, where you can build class without magic methods - use that way, avoid magic methods if you can.
2. If you can't describe class in interface - class was designed wrong.
3. Registry is bad pattern. If you need registry - something is wrong in your design.

Good book about patterns and design