My Kid Niki: Radical Ninja / Kaiketsu Yancha Maru collection

It includes all three Famicom games, but I only have the box for part two. There are also a couple copies of the NES game, the Japanese Game Boy game, and the Commodore 64 version (I still need the Apple IIe version, though). The big circuit board is the U.S. arcade board, complete with bezel and two marquees. Not pictured is the arcade game's operator's manual, which a friend is borrowing.
My Goemon / Mystical Ninja collection

Notables here include an animation cel from the anime, and all the Famicom and Super Famicom games. It's not a complete collection, but I still love it. Not shown are the Goemon doll (I have two of 'em) and mini deck of cards that Working Designs gave out at E3 a few years back.
My Mega Man / Rockman collection (part 1)

Mega Man X3 is the only U.S. MM game that I don't have the box for. The Rockman 2 box is signed by Keiji Inafune. The NES cart in the lower right of the picture is a review ROM for Mega Man 4. Not pictured (because I forget to dig them out) is the Game Gear game (complete with box) and the Japanese version of Network Transmission for GameCube.
Mega Man / Rockman collection (part 2)

There are some DVDs and strategy guides mixed in with the games here. I have a complete version of Mega Man: The Wily Wars, but only the cart for Rockman Mega World. That toy shaped like X's helmet to the left of the GameCube Anniversary Collection is a virtual pet-style game.
Mega Man / Rockman collection (part 3)

This is mostly manga and soundtracks. The Mega Man NT Warrior VHS (in the large, Disney-style box) in the upper right is a promo video that Warner Bros. sent out before the anime started airing in the U.S. The video in the black sleeve below it was sent out by Capcom...it has a couple of Mega Man TV ads on it. The upper left of the pic has two art books. Also note the fairly old Japanese manga (from Rockman 6 & 7). Not pictured are a ton of action figures and other such odds 'n' ends.
My Mr. Driller collection

Fairly self-explanatory, but the two CDs at the bottom are soundtracks. The pink one is a two disc set with music from Mr. Driller, Driller 2, and Driller G. The other CD is a single containing the "Susume! Driller" theme song (aka, the "Dig A Chance" song). The NamCollection for PS2 contains the original Mr. Driller, so it's part of the collection, too.