I think the most significant RTS is StarCraft. Why? Becouse StarCraft made the second revolution in the RTS genre, and nobody made game ever since that can beat it. They play it on WCG! There are so many RTSs around, and they play StarCraft on WCG. I think that's a game worthy of significance.
I think Warcraft 3 f*cked the whole genre for implementing heroes in the gameplay. Apparently you could beat the missions without strategy, if you had a strong hero. A strategy game without strategy. And the gaming industry just kept releasing games like this named RTS. Discusting....
And Doom, yeah, that was a great game. I remember playing it with friend in hot-seat mode

for days. But the all-time favorite is Duke Nukem 3D!!!
Nothing is comperable to "Hail to the king, baby!"