How can I control (start/stop) applications and services that start up after reboot?

Solution 1:

Applications and Menu Bar items

Most of these can be easily configured in:
System Preferences → Users&Groups → Login Items

LaunchAgents and LaunchDaemons

Some applications are cannot be configured in the System Preferences (e.g. Sophos AV Scanner, HandsOff Firewall,...) It's best to configure them in their own application to assure that everything runs as designed and intended.

You can look for related LaunchAgents and LaunchDaemons in:

~/Library/LaunchAgents               ~/Library/LaunchDaemons
/Library/LaunchAgents                /Library/LaunchDaemons
/System/Library/LaunchAgents         /System/Library/LaunchDaemons

Startup Items

After I installed the multi-boot utility rEFIt, it copied a file rEFItBlesser which is run at startup. Items that run at startup can be found in the following locations:

~/Library/Startup Items
/Library/Startup Items