The book of time travel is featured within the movie, as well as a new page if I'm not mistaken.
In the assembly scene, Donnie sees things speed up, which I thought was pretty cool.
At the end, in the car with Gretchen, he doesn't hear her say "What if you can go back in time and take all those bad memories etc etc"
The soundtrack is changed.
The rest you can find in the deleted scenes of the DVD I believe. And the impaling scene IS NOT in there! Whew!