The scene in AOTC where Anikin, C3PO and Amidala are going through the metal works on the conveyor belt.
U571 depth charge scene also good, but found that the fixed cutoff frequency of my dads DAV800 system was below the frequncy of the 'boom' on screen and so it sounded a bit 'thin'. I'm sure it will sound good on any system where the sub has variable cutoff.
U-571, The Matrix (that green WB sweep at the beginning is cool for starters! There's the bit where Neo causes space and time to bend as well, hehe...) and Ice Age; not many, but there are a few very cool sub moments in that.
I have heard Titan AE is good in this respect also. My next "purchase" I think...