At which point in the games was he at his best in physical ability and skill?
Was he in his prime in the first game? or when he was Big Boss?

Solid Snake =/= Big Boss. He was at his prime in Metal Gear 1 & 2, I'd say. He'd already retired by the time of the events of MGS.

...When was he Big Boss?

I would guess he was in his prime in MGS1 through MGS2. He was never Big Boss.

Probably during the NES games.
 
Edit: I just realized how old they make him seem in MGS4. If he was born in 1972, and MGS4 takes place in 2014, he'd only be like 42. They make him seem like he's in his 60's in the game...
 
Edit Again: I just read how the crap in his body caused him to age prematurely.

Snake or plistken in that game was quite out of shape in MGS2. MGS1 he came out of retirement so he was a little off his prime then. I think he was really at his prime when he killed big boss.

MGS2 is his bad ass point for me.
But MG is his prime

His prime is hard to pinpoint. I think it's probably after the events of MGS1.

Ok, I'm going to change my answer to Metal Gear 2. He was completely green in MG1 so I don't think he could be in his prime then. But in MG2 he had a few years in him.

" @Psykerstar:  You need to read the GB page for MGS3.  I think Solid Snake was at his best during MGS2.  You know, when you barely got to play as him. "

Yeah

"  He was at his prime in Metal Gear 1 & 2, I'd say. He'd already retired by the time of the events of MGS. "

" Ok, I'm going to change my answer to Metal Gear 2. He was completely green in MG1 so I don't think he could be in his prime then. But in MG2 he had a few years in him. "

" @Adamantium said:

"  He was at his prime in Metal Gear 1 & 2, I'd say. He'd already retired by the time of the events of MGS. "

"

" @Origina1Penguin said:

" @Psykerstar:  You need to read the GB page for MGS3.  I think Solid Snake was at his best during MGS2.  You know, when you barely got to play as him. "

My bad i thought that Boss was big boss its been a while since i beat the game "

When he was a creepy 40 year old dude staring at Meryl's butt.
 
"Damn right I'm gonna hit that."

Solid Snake is always in his prime. Also, really dude? Solid Snake is not Big Boss, not in the slightest (unless you count cloning. Which I don't!).

" @Coltonio7:  When he killed Big Boss at the end of mgs snake eater i thought he became Big Boss "

For me it would be MGS 1, he was probably at his peak then.

MG took place in 1995, Snake was 23 
MG2SS took place in 1999, Snake was 27 
MGS took place in 2005, Snake was 33 
MGS2 took place in 2007 and 2009, Snake was 35 and 37 respectively 
MGS4 took place in 2014, Snake was 42.   
 
My opinion, his prime was MGS1. Not too young, not too old and still in good shape. You can draw your own. 
  
Big Boss's exact year of birth was never confirmed (sometime in the 30s) but it's assumed that he was in his thirties in MGS3 and MPO and probably his forties in Peace Walker. He and Snake are not the same person. 

When he flipped burgers @ McDonalds !

So Naked Snake the one in MGS 3 the Portable Ops and MGS 4 is the Big Boss 
and Solid Snake is from MGS 1 and MGS2

MGS1

You obviously have no clue what you're talking about. 
 
Solid Snake is not Big boss. 
Naked Snake is. 

" or when he was Big Boss? "

" So Naked Snake the one in MGS 3 the Portable Ops and MGS 4 is the Big Boss  and Solid Snake is from MGS 1 and MGS2 "

MGS1 for sure. I thought Solid Snake was just the coolest. In his prime and ready to take on fucking 50 foot robots. And i don't think he was the same as Big Boss?

Solid Snake and Big Boss/Naked Snake are not the same person, technically.
 
I know this and I've never played MGS.

" @Psykerstar said:

" or when he was Big Boss? "

Hahaha, what?! You HAVE played these games, right? Its a different dude. 
@Psykerstar said:

" So Naked Snake the one in MGS 3 the Portable Ops and MGS 4 is the Big Boss  and Solid Snake is from MGS 1 and MGS2 "

NO. For God's sake, Naked Snake- who later became known as Big Boss was only playable in Snake Eater and Portable Ops. From Metal Gear to MGS4 its his clone- Solid Snake. You never even mentioned the two original MSX games. I'm willing to bet that the OP has never played a single MG game. "

never had a prime

" @MysteriousBob: The MG Games for the SNES? "

" @MysteriousBob: I apologize i meant the NES.  And you said "You never even mentioned the two original MSX games." So i assumed you meant the one for the NES that YOU didn't even know about apparently. 
 

  

"

" @Psykerstar: that was a prequel, that was naked snake and he killed the boss earning the title big boss "

" @Metroid545 said:

" @Psykerstar: that was a prequel, that was naked snake and he killed the boss earning the title big boss "

I knew that you needed to kill big boss and you became big boss and that MGS 3 was a prequel but i was confused about the whole Solid and Naked Snake thing which is why i thought that Solid snake was big boss i am sure once i play MGS 4 i will understand better "

" @Psykerstar said:

" @Metroid545 said:

" @Psykerstar: that was a prequel, that was naked snake and he killed the boss earning the title big boss "

I knew that you needed to kill big boss and you became big boss and that MGS 3 was a prequel but i was confused about the whole Solid and Naked Snake thing which is why i thought that Solid snake was big boss i am sure once i play MGS 4 i will understand better "

NO.
 
YOU NEVER KILL BIG BOSS, YOU ARE BIG BOSS. YOU NEVER KILL YOURSELF. YOU KILL "THE BOSS" AND GET THE TITLE OF "BIG BOSS". IN METAL GEAR 2 SOLID SNAKE (seemingly) KILLS BIG BOSS. PLAY THE ACTUAL GAME DAMN IT.  'sigh' I'm sorry, but I don't know why you've started a topic on a series of game you obviously know nothing about. MGS4 exists only to answer the questions from the previous entries. Considering you've obviously never played any of the Metal Gear games before, I suggest you at least play though all the other Solid games before attempting to play 4. "

Obviously you've only played Super Smash Brothers Brawl.

I'm compelled to do a super bump here because I don't think there was a clear explanation of who was who.  
 
Solid Snake is Big Boss' son. Hes a genetic clone of Big Boss. Solid Snake is also a twin brother of Liquid Snake. Solidus Snake is another clone of Big Boss (the third clone), but he is genetically the same as Big Boss (so he looks the exactly same) whereas Solid and Liquid were modified slightly. All 3 clones have accelerated aging issues. Solid Snake (aka Old Snake) is only 42 when the events of MGS4 happen but he looks much older because of the aging. Solidus Snake was likely in his 30s when MGS2 happened, but he also looked much older than he actually was. 
 
------------------------------
 
The Boss was Big Boss' mentor. She was a World War 2 hero. At some point she gave birth on the battlefield to Ocelot, and thats how she got her scar. The father of her child was The Sorrow, and she ended up having to kill The Sorrow (a Russian) on the battlefield at some point. She died in 1964 at the hands of Big Boss.
 
Big Boss (aka Naked Snake, aka Jack; protagonist of MGS3, Portable Ops, Peace Walker; antagonist of Metal Gear 1 & 2) was 29 in 1964 (MGS3) when he had to perform Operation Snake Eater as part of the FOX unit. He was extremely bitter with the way things played out because he was tricked into killing The Boss just to save America's ass for delivering nukes to a lunatic (Colonel Volgin).  He eventually leaves FOX
 
In 1970 (Portable Ops) he is kidnapped and held in a base on the coast of Columbia by FOX because its believed that Big Boss has part of the philosopher's legacy (an enormous amount of money, something which was to be retrieved during Operation Snake Eater). During this time he meets Roy Campbell and together they escape and recruit soldiers to form what would become the successor to the FOX unit, FOXHOUND. The FOX unit was disbanded after 1970. 
 
In 1972, Major Zero (who ran Operation Snake Eater in 1964) had initiated a project to create a clone of Big Boss because he was considered to be the perfect soldier. During that time, EVA (the female spy that Big Boss works with during Operation Snake Eater) gives birth to Liquid Snake and Solid Snake. Solidus Snake is born after 1974 using another method of cloning. 
 
Peace Walker occurs during 1974 after Big Boss has left FOXHOUND and The Patriots (an organization to influence the world set up by Ocelot, Big Boss, Major Zero, SIGINT aka Donald Anderson, Para-Medic aka Dr Clark, and Eva), upset at the way Major Zero is running things at the CIA. Kaz Miller (aka McDonald Miller) and Big Boss end up forming a Private Military Corperation called MSF. This PMC ends up turning into Outer Heaven. The public does not know that Big Boss is running Outer Heaven at this time. 
 
Big Boss returns to command FOXHOUND sometime before 1995. 
 
Solid Snake joins FOXHOUND and in 1995 hes given his first mission, to infiltrate Outer Heaven and rescue Grey Fox. He ends up discovering Metal Gear, and destroys it. Big Boss then reveals himself to Solid Snake as the leader of Outer Heaven, and its then that Solid Snake defeats him in battle, and with Big Boss apparently dead, Snake escapes and Outer Heaven is blown to pieces with an air strike. 
 
In 1999 Solid Snake is sent on a mission to Zanzibar land where it was suspected another Metal Gear was being developed. This time hes commanded by McDonald Miller (aka Kaz). He finds Grey Fox is the pilot of the Metal Gear and defeats him. Big Boss appears again, still alive as a partial cyborg (the same technology that Raiden and Grey Fox eventually have in them), and reveals himself to be Solid Snake's father. Solid Snake torches Big Boss with a flame thrower. 
  
In 2005, the Shadow Moses incident occurs, when Liquid Snake, the twin brother of Solid Snake and son of Big Boss, demands to get the remains of Big Boss so he can create an army of genetically modified soldiers enhanced with Big Boss' DNA. Shortly before Solid Snake is sent on the mission, Liquid Snake kills McDonald Miller and impersonates him when talking to Snake over the codec during Snake's mission. Solid Snake, unknowingly is carrying a virus called FOXDIE which has been targeted to kill Liquid Snake, and eventually Liquid Snake succumbs to the virus. 

After the Zanzibar land incident in 1999, Big Boss' body is retrieved by the Patriots, and his mind is hooked into the Patriots network so that Major Zero can show off his creation to Big Boss. Big Boss is in a hibernation state until sometime between 2009 and 2014 when hes rescued by Raiden and EVA (aka Big Mama). Hes put back together by using body parts from Liquid Snake and Solidus Snake. He meets Solid Snake in 2014 and is killed by the FOXDIE virus that Solid Snake has been carrying since Shadow Moses.  
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Heres some visuals of the different Snakes: 

@Psykerstar: mgs3 is set before solid snake was born and that is big boss you play as.

Snake was in his prime in METAL GEAR and METAL GEAR 2: SOLID SNAKE and NOT Snake's Revenge.

He was in his prime when he had his fist-fight with gray fox in the middle of a minefield. Gray fox was the 'Fox' in foxhound, meaning their very best operative as a result of his advanced reflexes and agility since he was the original test subject of the super-soldier project, and Snake was in his late twenties and had been in the military for something like 10 years (compared to gray fox's 30-40 ish years combat experience,) yet still managed to beat him.

Its mentioned by campbell at the start of MGS1 that "age hasn't slowed you down one bit" (speaking to snake) while Fox remarks "you haven't aged well." He probably got older but also wiser in that time but was out of action for nearly 7 years since killing gray fox. I'd still say the end of Metal Gear 2.

Ocelot's identical twin brother is the can of hairspray Solid Snake uses to kill Big Boss in MG2.