I'm going to assume that all the are straight up, arena-style fights. That said:
1 Superman vs Hulk - While Hulk's strength, durability and regeneration increases significantly faster than that of the Kryptonian, that is his only advantage. Superman starts off at a higher base level of strength and durability, he has an extreme advantage in speed and reaction time, he is more intelligent, and has a much higher level of mental speed(allowing for planning), and he actually has a relatively high level of training, from Batman, Wonder Woman, Wildcat, etc. Not to mention having a high variety of powers, giving him several venues of attack.
The fact that Superman has all of those advantages, along with the fact that you don't have to kill someone, to defeat them, makes Superman the winner.
2 Batman vs Captain America - In a straight up fight, with no prep. Cap wins every time. While Batman arguably has a higher level of skill, Cap is superior in every other way. Some things, like his strength, are only marginally superior, while others, like his speed and reaction time, are so far superior that it's not even funny. I can think of several scenarios where Batman would come out as the winner, but in a straight up fight, he doesn't stand a chance against Captain America.
3 Wonder Woman vs She Hulk - Far superior speed, far superior skill, far superior combat experience. 'nuff said.
4 Flash vs Quicksilver - I don't really think this one needs to be explained. Pietro won't even know what hit him.
5 Green Lantern vs Iron Man - This one depends on which version of Iron Man we're talking about, i.e. which armor. With the Extremis or later armors(especially the later ones), Iron Man has a fair chance of winning(the chance getting bigger with every new armor), but before Extremis, the odds would greatly be in favor of Green Lantern.
6 Martian Manhunter vs Vision - While the two of them have extremely similar sets of powers, the Manhunter's powers are generally superior to those of Vision. His speed is far superior, as is his demonstrated strength and durability, as well as his destructive power.
7 Green Arrow vs Hawkeye
8 Aquaman vs Namor - These two have pretty much identical powers, for the most part. Aquaman is demonstrably superior(by a pretty fair margin), in two aspects that puts the odds definitively in his favor, in a straight up fight. Namely, Speed and Telepathy.
9 Captain Marvel vs Thor - Not even a real contest. While the two have fairly close levels of physical capabilities, Captain Marvel is a pacifist with... let's be extremely generous and say 10 years of combat experience. Thor is a born and trained warrior, with the mindset that follows, who has thousands of years of combat experience.
10 Zatana vs Scarlet Witch
11 Lobo vs Wolverine - Stomp match.
12 Elongated Man vs Mister Fantastic - Superior in pretty much every way.
13 Deathstroke vs Deadpool - Like the above, Deathstroke is superior in pretty much every way, with the exception of Healing Factor. But you don't have to kill someone, to defeat them. Easy win for Slade.
14 Catwoman vs Black Cat - Normal human vs. Enhanced human. Add in the probability manipulation powers, and Catwoman doesn't stand a chance, even with superior skills.
15 Tigra vs Cheetah - Stomp match.
16 Darkseid vs Thanos - Without the help of various artifacts and external power sources, Darkseid can, in terms of powers, do everything that Thanos can do, and several of them he can do better than the Titan, as well as a few things that Thanos can't do. In a straight up fight, with no external power sources. Darkseid wins every time.
17 Lex Luthor vs Doctor Doom - Stomp match.
18 Green Goblin vs Joker - Stomp match.
19 Red Skull vs Ra's Al Ghul
20 Solomon Grundy vs Venom - Depends on which version of Grundy. If we're talking the version that Batman occasionally deals with, then Venom stomps. If we're talking about the version that usually goes up against the Justice League, then Grundy stomps.
21 Power Girl vs Ms Marvel - Stomp match.
22 The Atom vs Ant Man - Same power, but more effective.
23 Hawkman vs Archangel
24 Black Canary vs Black Widow
25 Red Tornado vs Whirlwind
26 Cyborg vs War machine
27 Nightwing vs Winter Soldier
28 Sandman vs Clayface - Stomp match.
29 Gorilla Grodd vs Doctor Octopus - Telepath vs. non-telepath(with no psionic defenses being part of his regular equipment or power-set), 'nuff said.
30 Doomsday vs Juggernaut
31 Sinestro vs Loki
32 Nekron vs Ghost Rider
33 Black Adam vs Ares - Stomp match.
34 Bane vs Kraven
35 Bumble Bee vs Wasp
36 Brainiac vs Ultron
37 Man Thing vs Swampthing
38 Dr Polaris vs Magneto
39 Guardian vs Captain Canuck
40 Captain Boomerang vs Boomerang
41 Silver Banshee vs Banshee
42 Hawk Girl vs The Falcon
43 Red Robin vs Daredevil
44 Killer Croc vs Lizard
45 Raven vs Invisible Woman
46 Captain Atom vs Vulcan
47 Talia Al'Gul vs Elektra
48 Penguin vs Kingpin
49 Beast Boy vs Reptil
50 Black Manta vs Tiger Shark
In case you were wondering, my ADHD started kicking in around nr. 20 or so. Which is why I didn't add more detailed explanations for the later fights.
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