Items in /Library/LaunchDaemons and /System/Library/LaunchDaemons load when your Mac starts up, and run as the root user.
Items in /Library/LaunchAgents and /System/Library/LaunchAgents load when any user logs in, and run as that user.
Items in /Users/your-username/Library/LaunchAgents load only when that particular user logs in, and run as that user.
Keep your hands off of some: Of those five folders, the two located in the /System folder (/System/Library/LaunchDaemons and /System/Library/LaunchAgents) are for components included as part of OS X, and you should resist the temptation to remove or alter them—they're essential to keep your Mac running correctly.
Modify others as you like: As for the items in the other folders, feel free to browse through them and see what's there. You can modify them—for instance, to disable them or to change how often they run—but before you do, you should understand a few things about how they work.
When you start your Mac or log in, the launch items in the relevant folders are loaded (that is, registered with the system) unless they have a Disabled flag set. Thereafter, their instructions will be carried out until you restart, even if you drag the launch item to the Trash. To see a list of all the currently loaded launch items on your Mac, open Terminal (in /Applications/Utilities) and type launchctl list and then press Return.
If you want to stop a launch item from running without your having to restart, open Terminal and type launchctl unload followed by a space and the full path to the launch item. (An easy way to add an item's full path is to drag it to the Terminal window.) For example, take this code:
launchctl unload ~/Library/LaunchAgents/com.apple.FolderActions.enabled.plist
It unloads the launch agent that enables AppleScript folder actions. Repeat the command with load instead of unload to turn it back on.
Because most launch items run on a schedule or on demand, and because any of them could be disabled, the fact that something is present in one folder doesn't necessarily mean the process it governs is currently running. To see what's running at the moment, open Activity Monitor—but bear in mind that the name of a given process as shown in Activity Monitor might not resemble the name of the .plist file that tells OS X to launch it.
Try a helpful utility: For seeing what launch items do—or for enabling or disabling them, or for deleting them (except those in the /System folder)—without any futzing in Terminal, my favorite tool is Peter Borg's $10 Lingon X. There's also a less-expensive Lingon 3, but it can do its work only on the current user's launch items, which makes it much less powerful. Lingon X provides a friendly graphical interface rather than an inscrutable XML file, although you'll still need a little geek mojo to understand some of its capabilities.
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