Wow, I think that was the absolute hardest vote to decide. I ended up going with Ender's Game because a) I loved the story, b) it had more of a lasting effect in my mind after reading, and c) I know many people will vote against Card rather than for the Story.
War of the Worlds however, is not only a classic, but a classic that has stood up in almost every form of media in which it has been adapted. I can't think of a single version of it that I have not enjoyed (i.e the H.G. Wells novel, the famous Orson Wells radio drama, both movies).
That said, if I'm judging it purely on my experiance of reading the novel and its effect on me, then I'm still going to go with Ender's Game, as much as it hurts to vote against WOTW. I think for me, this poll is the headline fight, but we'll see.