Most surprising discovery/secret/unlock/experience in this game?

[livinin82]

I think for me it's between the alligator cap, and it being the only item you get by going across vines, the ways you can kill The End, or the kerotan frogs.

Honorable mention to being able to use Raiden's mask to fool everyone.

[starschwar]

That's tough. All the ones you mentioned are terrific. Maybe it was the incredible importance of the cave radio call with EVA and how it changes the story in such a big, yet missable way?

The one that took me the longest to find out (and not on my own) was that wearing white camo makes The Pain's hornets attack less. To simulate the way bee keeper suits do the same thing.

[Dirty Duck]

This might seem like an odd pick but for me when I first played it was the Sneaking Suit.

I was used to finding smaller items in lockers but it felt mad to me that Naked Snake's Sneaking Suit, which was the default in MGS1 and 2 narratively, was a missable item hidden in a locker in Groznyj Grad. Felt like a great reward for exploring the location when you're meant to be sneaking through it, and it being similar to The Boss' just in time for the final stretch leading up to her fight made it that much cooler to me at the time.

And for a more obvious one: GUY SAVAGE. Happening upon that on my first playthrough was a mad stroke of luck and it made such a strong impact. Shame Delta kind of ruined the vibe of it, though I appreciate it being back at all since it was only ever on the PS2 version, even if the magic isn't the same these days.

[NateDog]

This might seem like an odd pick but for me when I first played it was the Sneaking Suit.

I was used to finding smaller items in lockers but it felt mad to me that Naked Snake's Sneaking Suit, which was the default in MGS1 and 2 narratively, was a missable item hidden in a locker in Groznyj Grad. Felt like a great reward for exploring the location when you're meant to be sneaking through it, and it being similar to The Boss' just in time for the final stretch leading up to her fight made it that much cooler to me at the time.

I was just coming here to post this. Because I'm an idiot I had never actually found it in-game until I replayed it a couple of years ago on Vita and randomly thought "I wonder if anything is available in that locker that Raikov was in". That being said MGS3 was and still is by far my least replayed of the numbered MGS titles ignoring V so I suppose I only had 3 chances or so to find it before. Still ridiculously stupid of me though given I had looked at stuff like the Hot Toys figure over and over again and never said to myself "why didn't I have that suit in the game?".

I'll also go with giving poisonous food to The Fear, always gets a laugh out of me.

[starschwar]

I absolutely missed the sneaking suit on my first playthrough, that's a good one.

Ghosts in The Sorrow's river responding to specific ways they were killed - complaining about being shot below the belt. Criticizing Big Boss for the indignity of indirectly cannibalizing them by eating a recently fed vulture.

Being able to snipe guards in Groznyj Grad from the cliffs and they stay dead/tranqued when you arrive.

Blowing up the Hind replaces them with hovering platforms when you go to the cliffs - Freedom Fighters influenced?

Here's one I only noticed as recently as Master Collection: LBJ's voice changes. Although only one actor is credited, he sounds much more haggard in the finale than he did in the initial phone call with Kruschev. Perhaps a deliberate means of illustrating how crises like The Boss's defection can take a toll on political leaders?

[MGWSpike]

Blowing up the Hind replaces them with hovering platforms when you go to the cliffs - Freedom Fighters influenced?

Here's one I only noticed as recently as Master Collection:  LBJ's voice changes.  Although only one actor is credited, he sounds much more haggard in the finale than he did in the initial phone call with Kruschev.  Perhaps a deliberate means of illustrating how crises like The Boss's defection can take a toll on political leaders?

The hovering platforms are based on prototypes from the 1960s.

I have a theory about the Lyndon B. Johnson voice change. Originally it was the CIA Director who'd award Snake with the medal (source). They changed it afterwards but probably didn't bother re-recording the few lines for the US dub. The CIA Director is credited with a voice actor but he has no lines at all in Snake Eater (he just lets out "Mmmph" when Big Boss passes by him without shaking his hand).

Anyway, it's hard to single out one element that is most surprising about this game and other members already gave great answers to the question, so here are a few additional stuff you may not know:
- Snakes runs slower when moving in the mountain part of the game. Moving around while wearing a cardboard box fixes this.
- If you use the Binoculars to zoom on a target, then quicky switches to a pistol, Snake will precisely aim at said target. Therefore you can easily turn any pistol into a sniper rifle.
- You can get a full length life bar before the Ocelot boss fight. Just repeatedly run into a spiked trap, half heal Snake, wear the DPM camo, wait. Rinse and repeat.
- You can quickly defeat The Fury using only... the knife. It's risky but it makes quick work out of him (3 knife combos and he's done).
- When under the effect of a stun grenade, The Fear will see his stamina bar take damage if you use a lethal weapon (i.e. an AK) against him.
- The ending of the game was strongly inspired by the opening of The Rock. People usually know about the influence of this film on MGS1-2 but I rarely see it mentioned about MGS3.

[Agent]

Destroying food and munitions storage making the guards in the region hungry and low on ammo, and destroying the helicopter to make it not appear later. Not that surprising but interesting. The most surprising was probably the nightmare minigame.

[starschwar]

Blowing up the Hind replaces them with hovering platforms when you go to the cliffs - Freedom Fighters influenced?

Here's one I only noticed as recently as Master Collection:  LBJ's voice changes.  Although only one actor is credited, he sounds much more haggard in the finale than he did in the initial phone call with Kruschev.  Perhaps a deliberate means of illustrating how crises like The Boss's defection can take a toll on political leaders?

The hovering platforms are based on prototypes from the 1960s.

I meant the gameplay mechanic.  In Freedom Fighters, accomplishing secondary objectives on one map would affect the other maps of any given chapter.  Blow up a helipad - no helicopters in the other areas.