LaunchAgents are only invoked when the user logs into a graphical session.
LaunchDaemons are typically launched when the system boots and are run outside of a specific user session.
The launchd manual page lists these folders with short descriptions:
~/Library/LaunchAgents Per-user agents provided by the user.
/Library/LaunchAgents Per-user agents provided by the administrator.
/Library/LaunchDaemons System-wide daemons provided by the administrator.
/System/Library/LaunchAgents Per-user agents provided by Mac OS X.
/System/Library/LaunchDaemons System-wide daemons provided by Mac OS X.