Always use Autoload if you can for large projects. The DRAMATIC performance losses of requiring files and classes you do not ever use during a page load can be pricey. Rasmus' quote was saying that PHP/APC can't save the opcode for a file WITH all of the includes if there is any conditional associated with the require. This means that each include's opcode will be pulled from cache each time (not a big deal!!!). [2006, http://pooteeweet.org/blog/538/]
Things in favor of Autoload:
1) Ease-of-use of not worrying about if your class is available
2) If you don't use Autoloading and require clases, you have to load all of those from the opcode cache (and make APC keep track of them) despite that you may not be using many of those classes at all.
3) It helps encourage putting things in classes (whether they are static functions or not).
4) If you ever need to conditionally require a class, you are likely going to run into the same opcode cache hits (instead of NOPs) as Autoload. You'll have to include ALL of your classes to avoid the problem.
Things in favor of Autoload:
1) Ease-of-use of not worrying about if your class is available
2) If you don't use Autoloading and require clases, you have to load all of those from the opcode cache (and make APC keep track of them) despite that you may not be using many of those classes at all.
3) It helps encourage putting things in classes (whether they are static functions or not).
4) If you ever need to conditionally require a class, you are likely going to run into the same opcode cache hits (instead of NOPs) as Autoload. You'll have to include ALL of your classes to avoid the problem.