the way i see it there are 3 ways to approach this task, which is just a precursor to watching all 1000 of the films on the NY Times list.
1. The Completist Method. you watch every single film on the list in some pre-determined order, such as alphabetical or chronological (which would be ideal), so that you can be completely sure you've seen all 100. this refreshes your memory of the ones you've previously seen. of course, there is the problem of not being able to track down the films that have yet to be released on DVD.
2. The Not-So-Completist Method. working under the theory that certain films do not necessarily need to be seen again in order to achieve the goal, the viewer is given a pass on certain films they've seen numerous times already. for example, i have a standing tradition of watching the Godfather every year on Thanksgiving. it's then safe to say i can skip those in the list.
3. The Rational Easy Way Out Method. you watch the ones you haven't seen, taking care of include any film you're not positive you've seen in its entirety. this begs the obvious question: just because you watched it when you were 8, does that mean you've really seen "Pinnochio"?