I will have to second Ghost in the Shell. Some new recruits were added to the Section 9 team in the 2nd season, so players wouldn't have to be limited to the main characters.
I ran a highly-successful campaign based directly on the original Deus Ex PC game. It was too much work for me though, and got burned out after six months because of converting the missions to d20. I highly recommend this game if you are into sci-fi conspiracy themes such as X-Files, Dark Matter, Ghost in the Shell, or the Matrix.
How about d20 Battletech? I love the setting, but hate the clunky battletech and mechwarrior rules systems.