Jamesds
Great Scientist
Is this being kept up to date? 
A couple of my favourites that I've not spotted in the main list:
NetBeans IDE (development) - Powerful IDE that supports many languages and frameworks, including Java, C/C++, Ruby and Ruby on Rails.
OpenTTD (entertainment/games) - Open-source clone of the Microprose classic Transport Tycoon Deluxe, a game I really enjoyed alongside Civ when I was younger
7-Zip (utilities) - reads almost any compressed format and saves to the main ones, including its own (.7z) which has a high compression ratio.

A couple of my favourites that I've not spotted in the main list:
NetBeans IDE (development) - Powerful IDE that supports many languages and frameworks, including Java, C/C++, Ruby and Ruby on Rails.
OpenTTD (entertainment/games) - Open-source clone of the Microprose classic Transport Tycoon Deluxe, a game I really enjoyed alongside Civ when I was younger
7-Zip (utilities) - reads almost any compressed format and saves to the main ones, including its own (.7z) which has a high compression ratio.