Just recently, I've done the epic book quest 3.1.4 (volume 3, book 1, chapter 4) in which you actually have to choose between 2 options that matter!
Background: Elrond has sent you to gather the rangers of Esteldin to form the Grey Company to come to Aragorn's aid. Halros, however, feels something's brewing in the Shire but can't decide whether to stay or go. That's where you come in.
Halros should stay
If Halros stays, the Grey Company has less people, which could turn out badly. We all know the shire is gonna be attacked though, so maybe some rangers to defend it would be helpful.
But those who have read the books know: Sharky will come anyway. Will this mean Halros will die?
Halros should go
If Halros goes, the shire stays unprotected from certain attack. More hobbits will probably die.
Halros will join the Grey Company, so Aragorn will have more men. (But some speculate that he will still die.)
In the end, either choice is fine as I don't think Turbine would let one choice be significantly better than the other.
So far, the only difference in the plot is Lotho's reaction, but I (and other people) expect it to have an effect in later books.
I'm glad Turbine tries to put some (probably) meaningful choices in the storyline and I hope it'll have a decent effect on it (and for more choices to follow).
For those interested, on my main cappy I chose for him to go and on my hobbit I'll choose to let him stay.