BES is "BlackBerry Enterprise Server". Most large organizations with a big fleet of BlackBerry's use this network product to manage the devices.
Javaloader is a utility that is shipped with the BlackBerry JDE. It is really a developer tool that allows us to load software on the device when testing (among other things, like view the file system on the device or erase it).
To use javaloader, you also have to install the BlacBerry desktop product for your devices - it installs a USB driver that is required.