When you're in the cave area with Meryl, hit her and quickly equip a cardboard box. She'll order a wolf to attack you, but if you're in a box, a wolf will pee on it instead. Now whenever that box is equipped the wolves will no longer attack you.
Lay any book on the ground, then go into first person view. Look at the magazine and you will see Alexander Roivas from Eternal Darkness: Sanity's Requiem.
Go into Otacon's lab (where you fought the ninja), then go to the middle desk and look at the monitor. There you will see a Gamecube with a WaveBird controller next to it.
In Otacons lab, you can find Mario and Yoshi figurines on top of a computer monitor. If you zoom in on Mario's head and shoot it, a 1-up message will appear over his head.
You can use the cardboard boxes you find for transportation. Simply equip the cardboard box that corresponds with where you want to go (there are three boxes in total - one labeled 'Helipad,' one labeled 'Nuke Building,' and one labeled 'Snowfield') when you are inside the back of one of the parked trucks. Eventually, a guard will appear, and you will be transported to the area labeled on your box.