The reason people probably cite FOTR so often is that it kind of stands on it's own a little better than the other two, which kind of blend together. Fellowship doesn't have concurrent storylines going on and that can be a pretty big strength.
Let's face it, when people only cite one movie they're usually trying to honor the whole trilogy, that's what the Academy did to ROTK and it's what end of decade list people are doing with the first.
I for one probably found ROTK to be the most satisfying, but I usually just like to look at it as a trilogy.