Mac OS X has cron. I don't know all of the Unix underpinnings and stuff to know what apps are doing behind the scenes, but I can tell you that you can install apps anywhere you want, but you can't move Apple's apps because Software Update relies on them being in your Applications folder or your Utilities folder.
For example, I have a separate games folder just for games, but it's not in my Applications folder, the game stores game progress inside a folder that's in the individual game folder. Almost all apps store it's settings in the user's Preferences folder. These are just automatically created when you launch the app for the first time and any setting that you apply that differs from the defaults will save in that preference file. If you remove that preference file, the app won't break, but you'll be back to the default settings again.
One thing that's really cool about Mac OS X is that if you're moving existing apps to a fresh install, you can just drag the application's icon over and if you want to keep all the settings for that app, just drag over it's preference file. Usually, when I do a fresh install of an OS, I'll drag over my entire user preferences folder and then I'll copy all the apps that I want.
There's only a few apps that I know of that aren't like this. Adobe apps and Quark. Those apps have to be re-installed because they install supporting files in multiple locations and even copying those doesn't seem to do the trick.
There are other apps that store content beyond the application package too like GarageBand. This is because it stores Sounds, Instruments and Loops in the root Library folder for other apps to use (such as Logic). This way, no matter which user is logged in, they have access to the same sounds and loops. GarageBand stores all of its files in /Library/Audio/.
If you have any more questions, I'll be happy to try to answer them for you.
