Mission Secrets, and what they unlock

Mission 1 Colorado Rockies
When you find the H11 crate in the cave near the waterfall ravine you will unlock the "Colorado Rockies" arena.

Mission 3 Colorado Interstate 70
When you get the Binoculars out of the crate in the back room of the first tunnel you will unlock the "Caves" arena.

Mission 8 C-130 Wreck Site
Kill Archer with one shot as he rides the chopper (good luck) and you will unlock the "Jungle" arena. Also, if you beat this mission in less than 3 minutes you will unlock the Syphon Filter 1 characters for 2 Player mode.

Mission 9 Pharcom Expo Center
When you find the Girly Mag in the locker you will unlock the "Pharcom Incubator Lab" arena.

Mission 11 Moscow Club 32
If you kill all three body guards on the dance floor in the beginning before they toss grenades you will unlock the "Disco Basement" arena.

Mission 12 Moscow Streets
Get the PK-102 from one of the white cars that try to flatten you and you will unlock "Rhoemer's Bunker" arena.

Mission 13 Volkov Park
If you can get to the first car before the agent blows it up you'll find a Biz-2 inside. This will unlock "Surreal" arena.

Mission 15 Aljir Prison (Break-in)
If you can make it through the whole level without the crossbow you'll unlock the "Aljir Prison" Arena.

Mission 18 Agency Bio-Lab (Escape)
When you enter the Operating Room you will unlock the "Agency Computer Lab" arena. You get to the Operating room by entering the ventilation shaft that you exited last in the previous mission -not the second one that leads out into the hallway.

Mission 19 New York Slums
Find the Dirty Laundry in the washer in the burning building. This will unlock "D.C. City Park" Arena.

Mission 20 Slums District
If you make it to the top of the stairway in the parking garage you will find a crate with an M-79 inside. This will unlock the Syphon Filter 2 characters for 2 Player mode.