Games like Monster Maker came in an extra thick jewel case, to fit an extra thick manual. You can't replace the door with a standard one.
I know exactly what you're talking about. I've run into Saturn games like that as well.
The Arcade Card Pro came in a thicker than usual case too I believe. Not sure about the AC Duo (maybe standard sized case).
Other items I can think of are:
Hyper Catalogs 1-6, DUO-RX catalog (same demos as Hyper Catalog 6)
Tengai Makyou Kabukiden demo mook (magazine/book)
Legend of Xanadu demo mook
Emerald Dragon demo mook
Lodoss War 1 mook (comes with actual game)
Lodoss War 2 demo mook
Lodoss War 1 & 2 also came in double jewel cases (possibly with maps or other extras, but I don't have the games in front of me)
Artist Tool - don't remember exactly, but I think the booklet is too big for the standard HuCard case.
Tsuru Teruhito no Jissen Kabushiki Bai Bai Game - Comes with a book about as thick as the HuCard case that I think includes stock info and companies from the game. I'm probably wrong about that, but there is an extra booklet.
http://www.pcengine.co.uk/HTML_Games/Tsuru_Teruhito.htmThere's also one Mahjong game by Face that came with a VHS tape. Don't remember the name of the game though.
I'm sure there's more, but that's all I can remember.
- akamichi