Metal Gear Solid 2: Sons of Liberty also had a two-disc case. For the version with the bonus DVD, anyway. Not sure if they all came with that or not.
It's odd that the NTSC release is only a 3-disc case with a paper sleeve for the fourth disc. Did they feel that the American audience would not buy a double-width case? Just doesn't seem to make any sense why they'd release it differently in the two regions.
I can't think of any games with a 3-disc flap, only a few with 2-disc ones. You could probably find a normal dvd case with a 3-disc flap, and just hope that it'll have the same clips as a 360 case. It won't all be translucent green, but would still be better than a paper sleeve.
What was the bonus pre-order disc with Dawn of Mana?
And straying off-topic, are there any freeloader type discs for the PS2? I have Dawn of Mana, which never got a PAL release, but I don't want to hard-mod my PS2, and playing it on an emulator on the PC is getting annoying...