EDIT: Added N64 boxes, all in pretty good condition, ask for specifics.

UPDATE EDIT: So it appears that I've still got plenty of boxes lying around here, the large purchaser has flaked out on the sale. So, here's what's left.

Digimon Racing
DBZ: Buu's Fury
2 x DBZ: Supersonic Warriors
Dual Masters Sempai Legends
Final Fantasy Tactics: Advance
Harry Potter & the Prisoner of Azkaban
The Incredibles
Ms. Pac-Man Maze Madness
Mighty Beanz (with the bean)
2 x Megaman Battle Network 4: Red Sun
Megaman Battle Network 4: Blue Moon
Megaman Battle Chip Challenge
Pokemon Sapphire
Pokemon Ruby
3 x Pokemon FireRed (all with Wireless adapters)
Shrek 2
2 x Spider-man 2
Spongebob: The Movie
Spongebob: Battle for Bikini Bottom
Sword of Mana
Spyro Orange
Yu-Gi-Oh: The Sacred Cards
2 x Yu-Gi-Oh: World Championship Tournament 2004
Zoids: Legacy
GBA Video: Pokemon For Oh-ho the Bell Toll
GBA Video: Pokemon Jhoto Photo Finish

N64 boxes:
Goldeneye 007, players choice
Waialae Country Club
WCW vs. nWo
Madden 64

$1.50 each, all come with instructions, most have registration cards and warranty junk, GBA instructions, etc. Anyone who buys 10 or more will get free shipping.