I broke the nusoap.php class out into 9 seperate files, one for each class as most people organize their libraries. I then included the 1 nusoap file, then recorded the time, then included the 9 nusoap files and recorded the time. After 50 iterations the average was that including multiple files was on 24% slower than the one large file.
So what's the lesson? If you're distributing your PHP software package and/or push your scripts to a live server, think about combining your classes by directory into one big file. Lets say you have a directory like this
If all of those files have to be included to create a user object, just create a master user.php file with all of your classes built into that file. The upside is a little faster performance and easier/less includes. The downside is it might be slightly harder to maintain. The trade off is decided by your traffic load. Some of your out there like to eek every little nano second you can out of your scripts. :)