I'd imagine that most people would say the Holmes fight as it was so one-sided but Holmes eased off on Ali for large parts of the fight and a lot of his head punches were blocked by Ali's gloves. There weren't many times where punches caused Ali's head to 'spin' as it were. I think Ali absorbed far more punishment in his first fight with Frazier than in any other. He took a lot from Shavers but that was sporadically. Frazier hurt him round after round in their first fight.
You're probably right about Frazier and Lyle. I know we're essentially talking about punishment to the head but Big George hit him with some hooks to the body that would've felled a bull. At the end of the fight Ali's brother grabs him around the waist to raise him in the air. Ali starts punching his brothers arms until he is released, he is in obvious pain.
Thrilla in Manilla. He didn't get knocked down or lose like in the first fight, but the heat and punishment were so great that he famously told Angelo Dundee "cut the gloves. I ain't taking no more of this ****." Or something like that. Really, he was never the same. Shaver, Lyle, and Young arguably all beat him, and Shaver and Lyle punished him good. Very sad. Not only was he already showing the beginning of Parkinsons, but he had a thyroid problem, medicine for it that harmed his reflexes, and a quack doctor that did not know what he was doing. Ali was really destined to end up a mess.
Another vote for Manilla ... too many factors added up to what should have been his swan song. Conditions (I've heard it was nearly 100 degrees in the ring), age, the relentless pace and the fact neither man was willing to stop or step back. He certainly took punishment in the FOTC, but he was also four years younger and hadn't been through the wars in the intervening years with Frazier (again), Foreman and Norton (twice). The body can only take so much abuse, and I think the resiliency was pretty much gone by Manilla. He survived and won, but nobody would have blamed him from stepping down and retiring after this punishment.
I can't really see any damage coming from Ron Lyle. In that one,Muhammad was in a lazy mood during the early rounds and Ron was picking up points from workrate. Simple as that. The single bout where Ali picked up most damage was the Larry Holmes one. Ali was already in terrible condition coming into the fight and was nothing more than a punchbag.
The fight against Trevor Berbick didn't do him any favours to be honest. Hence the beating Mike Tyson gave to Berbick for trying to knock his hero out.
When his wife surprised him in Manilla? Ali said a reason he took the fight to have sex with his mistress. I recommend the book Facing Ali. Its very good, full of contents and color quotes. You get to know his opponents too. Larry Holmes quote on Ali and women was a classic.
Frazier -3 Holmes Frazier 1 Shavers Spinks 1 Ferdie his doctor said he took an atrocious beating from Spinks in the first fight.
I don't think Ali did that because he was in pain. I just think he liked having a bit of space after a fight was over. A similar thing happened at the end of the second Norton fight with Bundini Brown. But then Bundini was a tw*t and I have no sympathy for him whatsoever.
I don't think Ali absorbed a really severe beating against Holmes. Holmes didn't land many clean head shots and went easy on Ali for most of the fight. But as it was completely one-sided with Ali doing virtually nothing I think it gets remembered for being a savage beating and I don't think it was.
Manila was the fight that had the most devastating effect on Ali but that was also down to factors such as temperature, lack of proper conditioning and the accumulation of punishment over a series of fights etc. But if you look at the fights in isolation and the punches that were absorbed, I think the first fight with Frazier was clearly the worst beating Ali took. But Ali was young enough to absorb it better than he would have done a few years later.