Crystalien Conflict (aka. that one Mars Mission game), the last and best flash Lego strategy game (in my humble opinion), which can be played offline also after download from website below.
Close favorites are Robo Chronicles, Treasure Trench and the three 2004 Alpha Team games: First Encounter, Drone Menace, Ogel's Fortress.
Almost all of the Old-School games can be downloaded from http://biomediaproject.com/bmp/lmp/
And almost all of the Bionicle games from