What affects the order of applications in Lauchpad?
On a clean install, the core Mac OS X apps are originally ordered alphabetically. Newly installed apps will be appended at the back on an empty spot starting with page 2 (they will never be appended on page 1, even if there is room available, but you can ofcourse drag them there).

Apps can then be arranged manually, and they should remain in the order you sort them. However, I have noticed quite some buggy behaviors, mainly apps changing position after a reboot, and MAS updates pushing apps of the page.

I hope these will get ironed out in a coming update.