I know that most all of the PC Engine games (both HuCard and CD) came simply with game, manual, jewel case, and spine card (for the CD games, but not for the HuCard games, I believe). I would like to create a comprehensive list of all of the PC Engine games which came in (like in a magazine) and/or with (like included extra stickers) something extra. The few that I know are as follows:
The below came in something larger than the standard jewel case.
3x3 Eyes - had a regular single CD jewel case release & one which came in a larger box with a VHS tape
Anearth Fantasy Stories (Seiya Monogatari) Taikenban - came included in Dengeki CD-ROM & BOOK Vol.3
Bakuretsu Hunter - came included in a Bakuretsu Hunter book, and you had to cut out the CD case front and back insert from the magazine
Forgotten Worlds - came in a larger box with an Avenue Pad 3 - a 3-button controller
Motteke Tamago - came included in Super PC Engine Fan Deluxe Vol. 2 magazine (This issue also included a PC-FX disk of some sort, I believe.) You had to cut out the CD case front insert from the magazine. This game did not have an official CD case back insert issued.
Pachio Kun Maboroshi no Densetsu - had a regular CD jewel case release & one which came in a larger box with a pachinko PCE controller
The below included something extra inside the regular jewel case sealed game.
Detana!! Twin Bee - sticker sheet insert
Galaxy Fraulein Yuna - had a double jewel case re-release with a HuVideo disk
Gradius II - sticker sheet insert
Legend of Xanadu - poster
Populous - HuCard game which had a spine card
Princess Maker - had a double jewel case release with a mini audio CD and guide book
Snatcher - sticker sheet insert and a biography/lore booklet
Street Fighter II - HuCard game which had a spine card
Tengai Makyo (Far East of Eden): Fun Kabuki Den - poster
Urusei Yatsura (Lum): Stay with you - had a regular single CD jewel case release & a double CD case release which included a soundtrack CD
*Edit: Added to the list.