The disc of ZOE1 is nothing special, but for the longest time I thought it's original design included a huge "tear" on it. Since the design looks like a circuit board, I though it looked cool that it had a part that looked like it was burnt out. Turns out my copy just had an actual tear in the sticker, but I didn't realize this for years.
But as for favorite, this Bayonetta disc instantly came to mind. Disregarding all the visual clutter, one look at this CD and I knew I was in for a wild ride.