In Moodle 2.x, on a dedicated Debian Linux Server
The way I like to upload large files is to use the Repository Plugin. Enable "Filesystem" module. In the "Settings" screen for this plugin, we can create a Repository pointing to a filesystem upload directory.
Create a directory under the moodledata/repository directory per course.
This directory should be owned and readable by the webserver user ( in LINUX - Debian 5.x: www-data)
Now use FTP or better SFTP to upload any files to this directory. You may need to enable group read-write permissions for the directory, so that other users can write to this directory.
Example: directory: /var/moodledata/repository/mynewcourse
As root user:
# groupadd mynewcourse
# chgrp mynewcourse /var/moodledata/repository/mynewcourse
# chmod g+rwx /var/moodledata/repository/mynewcourse
# adduser uploader
# usermod -a -G mynewcourse uploader
In the moodle web interface, when adding any resources, the file chooser now shows the Filesystem Repository that we created.