Love this question...it is a win win question for me because my favorite superhero is the Surfer. My second favorite is Thor (third is Blue Marvel).
When the two first met in Silver Surfer #4, it was clear that Thor was the more powerful of the two. It is also noteworthy that Stan Lee actually wrote that comic book, with the great John Buscema on pencils. Even amped by Loki's magic, the Surfer was no match for Thor. Interestingly, in The Mighty Thor 4, a reader wrote in and asked Stan, point blank, "Who is Marvel's most powerful superhero?". Stan's answer? "Thor!".
Unquestionably, Stan intended the Mighty Thor to be Marvel's top dog from the word go. Unfortunately, Stan retired as EIC in 1972. While Jim Shooter faithfully upheld Stan's vision of Thor as Marvel's premier powerhouse, the vision began to decay when Tom DeFalco took over, who for the first time in Marvel history, outrightly declared the Hulk to be superior in strength to Thor, but Thor to be the more powerful.
The Surfer and Thor clashed again in the Blood and Thunder arc in Silver Surfer #86, this time Thor was amped by the power gem and decidedly NOT holding back. The Surfer and Thor tangoed briefly; generally, that skirmish is ruled by fans as a win for Thor. My take was the Surfer was simply trying to slow Thor down, although unsuccessfully. It's not as if he were blood lusted. Thor went on to trade blows with Thanos, toe to toe, mano y mano in one of the most earth shattering fights between two heavy weights in Marvel history.
In 2007, after the Surfer had just been amped up by Galactus to a greater level of power, the Surfer went on to fight Beta Ray Bill in the Godhunter arc. The results were stunning. The Silver Surfer proceeded to literally beat BRB down. While he apologized. And with little effort. I've always seen BRB and Thor as fairly close in power and strength (although I have Thor up 2 to 1 in their fights). Nevertheless, for anyone who has a question these days about who might win in a fight between the Surfer and Thor, that fight stands as a possible outcome because of the similarity between Bill and Thor.
Finally, In Thor #4 last year, the Surfer clashed yet again with the Thunder God. While the outcome did not dictate a clear winner, I say it leaned slightly in favor of the Thunder God.
However, the aforementioned is an appraisal of these two titans in light of their fights in continuity.
However, a logical appraisal of these powerhouses respective set of powers might seem to favor the Silver Surfer these days. To me, clear advantages for the Surfer would lie in his obvious speed advantage. The Surfer is leagues faster than Thor, although Thor does have feats in continuity that demonstrate remarkable superhuman speed, but certainly not in the same league as a Superman and definitely not in the same league as the Surfer. The Surfer can phase. I don't know that Thor can counter that. How does Thor hit something he can't touch? Thor, on the other hand, has flashed some magical prowess, enough to counter Loki and on one occasion, Dr Strange. It's funny that Stan Lee never explored this aspect of Thor's powers more in depth. If Stan were competing with Superman in the powers department (as I have often felt he was...), it seems logical he would have capitalized on Thor's mystical/magical source of power as the antithesis to Superman's blazing speed. Is Thor's magical prowess enough to counter the Surfer's ability to phase or his insane speed? Questionable at best.
And of course, at this juncture, it is important to mention the Marvel universes version of a Green Lantern ring. Without Mjolnir, Thor is pound for pound, the strongest superhero in the entire Marvel universe (or at least, he used to be...). His durability in continuity shows him resistant to the adamantium claws of Wolverine and taking point blank explosions from nuclear bombs or doing battle in the heart of a star. It is important to note that Thor has control of the weather WITHOUT Mjolnir. Also, he is a skilled warrior.
With Mjolnir, he has the antiforce, the godblast, limited telepathic control over large crowds, invisibility, flight at 3x the speed of light, transmutation of elements and teleportation.
However, while the aforementioned facts seem to favor the Surfer, in my personal opinion, the Surfer is easily trumped by Thor when he is in possession of the Odin force. Rune King Thor is WAY, WAY out of the Surfer's league, in my opinion.
Having said all these things, I find myself wishing for the old days. I miss a Marvel universe that does not clearly indicate Thor as it's premier powerhouse superhero.
Just my two cents.
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