1. Starting the album "Wish You Were Here" at the beginning of "Jupiter and Beyond The Infinite". My favorite bit of it is that the cuts of the film when Dave's pod shows up in the mansion room are timed almost perfectly with the verse changes in Welcome To The Machine.
2. Starting "On the Run" right as the stripes of color begin to flash past during the warp scene of "JaBtI". (I got this idea from the video Roger Waters used for this song at his live show).
3. Syncing up Brain Damage/Eclipse so that the song ends as soon as the credits start rolling.
4. Starting "In The Flesh" so that the actual song (minus the little "Outside the Wall" segue bit) starts as soon as the MGM logo fades away (I've never gone any farther than this. Perhaps The Wall would be a good one to try as well?)
For some reason, "Jupiter and Beyond the Infinite" is the best part of the movie to monkey around with.
I've also heard that the studio disc of "Ummagumma", when played in its original order (which I'm not sure of, at the moment) syncs up well with the "Dawn of Man" sequence.
I'm anxious to see if any parts of the movie sync up with The Beatles' "Across the Universe". Seems like it would be appropriate for a sequence like "JaBtI".