-The Patriot (Boss's gun from MGS3) is available by obtaining the Big Boss emblem or by entering the password in the Extras menu.
-Mantis doll from defeating Screaming Mantis. Allows Snake to shake enemies once a projectile from the doll hits them. Shaking drops ammunition, grenades, or healing items as well as killing them.
-A custom 1911 that can be customized with a silencer can be obtained by entering a password in the Extras menu.
-A long barreled Desert Eagle can be unlocked by obtaining the Fox emblem or entering a password.
-"Emotions bullets" can be unlocked that affect certain enemies emotions and cause them to react accordingly. Obtained from Drebin's shop on 2nd playthrough.
-A "race gun" can be unlocked by beating the game. Poor power and range, but bullets ricochet, allowing the user to hit people behind walls.
-Smoke grenades that affect emotions, similar to the bullets. Can be obtained from Drebin on 2nd playthrough.
-Gun del Sol from Boktai can be unlocked by collecting all four Beast Dolls and the Frog Soldier figurine. Causes soldiers to drop items they normally wouldn't, up to 4. Also depletes psyche gauge.
-Sorrow doll can be unlocked by collecting it before you defeat Screaming Mantis. Allows user to manipulate the bodies of the dead.
-Thor .45 can be unlocked by entering a password or obtaining the fox emblem. Holds one bullet at a time but has massive power. Comes with a built-in dot sight.
-Type 17 pistol can be unlocked by entering a password or obtaining the Hound emblem. Machine pistol carries 10 rounds, semi or auto fire. Must expend whole clip before reloading.
-Scanning plug available from Drebin after 10 hours of MGO. Can be used when it is equipped and Snake has a PMC soldier held in CQC choke-hold. Allows user to see outline of all soldiers linked into the SOP system in the zone.
-Stealth camo is unlocked by beating game without initiating a single alert phase or can be purchased from Drebin for 5,000,000 DP from second playthrough onwards. Makes him invisible to naked eye, but scanning beams used by Gekko and Dwarf Gekko can find him. Enemies can still hear footsteps and if Snake bumps into an enemy or is hit by a bullet, the camo automatically deactivates.
-Bandana can be unlocked by not killing a single enemy or purchased from Drebin for 5,00,000 DP on second playthrough. Gives player infinite ammo.
-Camera can be found on Nomad during Mission Briefing. IF it is pointed at a Beauty during the "white world" phase, she will strike a pose for you. Can be used to hunt ghosts hidden throughout Act 4.

Costumes:

-Altair costume unlocked by entering a password or achieving the Assassin emblem.
-Bio Boss (wat?) costume can be obtained by getting the Big Boss emblem.
-Suit costume can be unlocked by beating the game once.

(Found these online, and I think they're from the strategy guide, but I figured some people want to know without buying a $20 book.)

Those of you that have the game, I envy you. Play it. For me. Your fallen MGS-less comrade

Guys I have the game. Best game of them all in Next Gen.