I'll list the most significant ones:
-Blue Planet Dilogy (Age of Aquarius and War in Heaven)
http://www.hard-light.net/wiki/index.ph ... f_Aquarius
http://www.moddb.com/mods/blue-planet-war-in-heaven
-Dimensional Eclipse
http://www.moddb.com/mods/dimensional-eclipse
-The Antagonist
http://www.moddb.com/mods/brandon-r
-Wings of Dawn
http://www.moddb.com/mods/wings-of-dawn
-Freespace Port
http://www.moddb.com/mods/the-freespace-port
-Just Another Day Collector Edition
http://www.hard-light.net/wiki/index.ph ... 7s_Edition
-Just Another Day 2.21
http://www.hard-light.net/wiki/index.php/Just_Another_Day_2.21:_You_Are_(Not)_Alpha_1