More memorable ones just off the top of my head: Emissary The Jem'Hadar The Search Defiant The Die is Cast The Way of the Warrior Paradise Lost Shattered Mirror A Time to Stand Sacrifice of Angels Valiant Tears of the Prophets The Changing Face of Evil What You Leave Behind I think that's most of the major ones anyway.
The Maquis part 2, Rules of Engagement, Nor the Battle to the Strong and the Emperor's New Cloak all come to mind too.