These are packages that I use and recommend on my Linux Ubuntu box.

System Tools

• Filelight
  Displays a circular graph of the space used by your files, so you know when you
  have big files (for example, images of your work) that if you backup them you’ll save space.
  sudo apt-get install filelight
• gdmap
  Displays space used by files, but with squares.
  sudo apt-get install gdmap
• gParted
  Interface for partitioning your hard disk drive, and make it a bit easier, without having to reinstall everything.
  sudo apt-get install gparted
• aptoncd
  Just for Ubuntu and Debian. Allows to backup your packages installed in a CD so you can have them ready to
  install in another computer.
  sudo apt-get install aptoncd
• htop
  sudo apt-get install htop

Programming/Editor Tools

• PDFedit
  Free (and open source) editor for manipulating PDF documents. GUI version + command line interface.
  sudo apt-get install pdfedit
• Bluefish
  sudo apt-get install bluefish
• Meld
  A simple but powerful small tool that can compare two files or directories and tell you the differences, or merge them.
  sudo apt-get install meld
• vim
  sudo apt-get install vim

Music Tools

• SoundConverter

Photo Tools

• sudo apt-get install xaralx

Networking Tools

• gFTP

Media Players

• Boxee
• Songbird
  How to configure songbird.
• VLC Player

Downloading Tools

• JDownloader
• Deluge, download it here.
  sudo add-apt-repository ppa:deluge-team/ppa
sudo apt-get install deluge

GUI

• Mac Dock For Linux?
• GnomeDo
  sudo apt-get install gnome-do gnome-do-plugins
• Compiz

Additional

• p7zip
  sudo apt-get install p7zip
• TaskCoach
• KeePassX
  sudo apt-get install keepassx
• ntp
  sudo apt-get install ntp
• ubuntu-restricted-extras
  sudo apt-get install ubuntu-restricted-extras

More Great Sites

This is great site to get applications

• Appnr

Other great lists of packages:

• Essential Ubuntu Productivity Apps
• Must have Ubuntu Packages from SuperUser.com
• Top 100 of the Best (Useful) OpenSource Applications