During the Act 1 FROG attack sequence, attack Meryl. She will say the same things she said when you attacked her in Metal Gear Solid.

The password Johnny puts in to disable the laser trip trap is "MERYL SILVERBURGH".

You fight Crying Wolf in the same area you fought Sniper Wolf.

You can find the Hind D still in the Snowfield where you fight Crying Wolf.

During the Mantis fight, switch your controller ports when your television switches to "Hideo 2". Otacon will come on the Codec and notify you that the trick does not work twice. You will also get a suggestion about destroying the bust.

When you die in Act 4, the "Game Over" music from the first Metal Gear Solid will play.

After you die during the final Boss battle and select "Exit", it quickly changes to "Exist". Liquid Ocelot says "Not yet Snake, it's not over yet" and it moves the pointer back to "Continue". This is a reference to a quote by Liquid in the original Metal Gear Solid.