You can use cron-apt to automatically download updates at a certain time, I think the default is 4am.
Some download managers have built in scheduling, but you can just as easily use crontab to schedule downloads at a certain time.
For a list of download managers in Ubuntu take a look at http://packages.ubuntu.com/search?ke...id§ion=all
d4x - Among others, its key features include proxy and SOCKS5 support, recursive downloading, wildcard matching, download scheduler
, multiple download queues and more...
kget - KGet is an advanced download manager with support for Metalink and Bittorrent. Downloads are added to the list, where they can be paused, queued, or scheduled for later.