I'm only making this guide since nobody else has yet, and some people might be wondering what the last few achievements are and how to get them. Most achievements in the game are unlocked just by completing the games themselves, but there's at least three that might be missed, the first of which is:

#1
Name: Cover-to-Cover Gear 1 & 2
Desc: Read all pages in the Screenplay Book

#2
Name: GO AHEAD SOLID SNAKE!
Desc: Start Metal Gear

#3
Name: Ultimate Weapon No More
Desc: Destroy Metal Gear

#4
Name: Supreme Commander Down
Desc: Defeat Big Boss in Metal Gear

#5
Name: No Big Deal
Desc: Complete Metal Gear
Note: this is unlocked specifically by reaching the ranking screen after the credits are finished, don't close the game until after that point or you will miss the achievement.

#6
Name: Outer Heaven Survivor
Desc: Complete Boss Survival in Metal Gear
Note: 'Boss Survival' is a mode unlocked after completing the game, it can be played on either Easy or Original difficulty and completed with any rank to unlock this achievement, so don't even worry about it.

#7
Name: Right On Time
Desc: Start Metal Gear 2

#8
Name: We Didn't Start The Fire
Desc: Destroy Metal Gear D

#9
Name: Your Number One Fan
Desc: Defeat Gray Fox

#10
Name: It's... Over
Desc: Defeat Big Boss in Metal Gear 2

#11
Name: Free from Rations
Desc: Complete Metal Gear 2

#12
Name: Zanzibar Land Survivor
Desc: Complete Boss Survival in Metal Gear 2
Note: As with the first game, 'Boss Survival' is a mode unlocked after completing the game, it can be played on either Easy or Original difficulty and completed with any rank to unlock this achievement, so don't even worry about it.