CONCEPTUALIZATION
Which Superman? Which Anakin? Win what?
Superman has had a number of quite distinct incarnations, some coexisting, others the only instantiation of the Man of Steel within their universe. Let's look at a few.
Golden Age Superman -- The original Superman, able to leap tall buildings in a single bound, outrace trains, and nothing less than a bursting shell could penetrate his skin. His creators quickly added new powers so that Superman could compete for the hearts and minds of America's youth among the burgeoning population of superheroes in the press. This Superman was revived as the aging "Earth-2 Superman" in the Silver Age and trotted out for several "event" series, most recently Infinite Crisis. His durability is primarily the result of the "toughness" of his skin.
Silver Age Superman -- This version truly was the zenith of humanoid potential; a genius, capable of casually exceeding the speed of light and juggling planets. He slowly morphed into the sub-type recognized as the Modern Age Pre-Crisis Superman, designated by the Creator of the Universe to have some special significance. This significance was never realized, however, has Pre-Crisis Superman was altered by the Crisis.
Post-Crisis Superman -- Unhappy with the Silver Age excesses, John Bynre "de-powered" the Man of Steel. Superman could now fly, lift mountains, and withstand nuclear explosions; but planet-juggling was beyond his capabilities, and his intellect was more like the average human's (although he had superb memory and the capacity to deal with much greater sensory input). His defenses are based on a bioelectric field that emanates several millimeters above his skin and hair.
Post-Infinite Crisis Superman -- The current version of Kal-El is still being explored, but we may make several assumptions about him based on the latest origin story in Birthright and the current writers' attitudes. Superman can now see auras around animals, prompting his adoption of vegetarianism. He is probably stronger than post-Crisis Superman.
All major versions of Superman are vulnerable to a rare radioactive element, usually called Kryptonite. Post-Crisis Superman is also vulnerable to magic.
ANAKIN SKYWALKER
Although there are not distinct versions of Anakin, there are several "points of view" about him.
The Early Point of View -- According to early materials, Anakin was a tall, hearty man who had developed excellent flying abilities before he met Obi-wan Kenobi. The elder Jedi Knight trained Anakin in the ways of the Force, and the two fought together during the Clone Wars. Anakin became convinced the best way to use the Force was the Dark Side; by concentrating anger, fear, and aggression, he could manipulate the lifeborne energy field that permeates the universe, granting him superhuman speed, endurance, reflexes, and strength, along with a panoply of other more mystical abilities. His friend Obi-wan tried to reason with Anakin and show him the folly of his ways, but Anakin attacked, and was forced into a molten pit. The molten rock or metal disfigured him, forcing him to live in a life-support suit with several cybernetic limbs. Over the years, he began to deny his life as Anakin, subsuming his identity to his new name and role of Darth Vader, Dark Lord of the Sith. Vader hunted down and destroyed nearly all the Jedi. He fought his son, Luke, several times. During their last encounter, Luke appealed to Anakin to recall his old identity and proudly referred to him as a Jedi. That awoke something in Anakin, prompting him to sacrifice his life for his son's. He briefly reappeared as a ghost, his physical wounds healed and a smile on his face.
The New Point of View -- Anakin was conceived by the midiclorians, microscopic symbiotes who mediate between the Force and sentients, probably under the direction of a Sith Lord. Whatever that Sith Lord's plans for Anakin were, they probably fell awry upon his assassination; Anakin was born a slave on the planet of Tattooine. In between grueling sessions of slave labor, Anakin managed to construct a pod car and become a famed pod racer. This attracted the attention of the Jedi, who took him away from his mother to be trained in their ways. The Jedi kept Anakin separated from his mother until, left unsupervised on Naboo, he returned to Tattooine to search for her. He arrived in time to find his mother bound in the camp of the nefarious Sand People, dying. After his mother's passing, he killed all the Sand People, then confessed his mass murder to his Nabooian crush. Suitably impressed, she married him. They kept the marriage secret for years while Anakin fought in the Clone Wars. Over time, he became convinced that she would die in childbirth. Told by a Sith Lord that the Sith use their "passion" for power, and that he could save her life, Anakin switched his allegiance to the Jedi's old enemies and murdered a number of Jedi children and trainees. Obi-wan Kenobi was sent to assassinate him, and very nearly succeeded; he left Anakin maimed and burning on a lava embankment. Only the newly-acclaimed Emperor's timely arrival saved Anakin's life.
Except it didn't. According to the new point of view, Anakin died some time around these events and became the separate person, Darth Vader. It is unknown exactly how Luke convinced this new person that he was identical to the old person, but he pulled it off, and Vader died believing he was Anakin. One would be pressed to look for a semantical or psychological loophole to this bizarre turn of events, but the intratextual and extratextual evidence (direct from creator George Lucas) is clear: Anakin died during Revenge of the Sith.
As Jedi are wont to do (except when they don't; see the Prequel Trilogy), Anakin's ghost appeared before Luke after Darth Vader's death. It bore the appearance of a young man, in accordance with the new point of view that Anakin died a young man.
VICTORY CONDITIONS
To answer the question, "Who would win," one must answer the question, "Win what?" There are many things one can win -- a heart, the lottery, Scrabble. I suggest personal combat. Anakin may wear his personal clothing and carry his lightsaber. Superman may wear his costume and carry no weaponry. The two will fight on an Earth-like planet covered predominantly in short grasses. Their other characteristics will be as follows:
Superman
Post-Crisis
Flight
Super-speed
X-ray vision
Heat vision
Microscopic/telescopic vision
Bioelectric aura
Super-hearing
Anakin
New point of view
Jumps high
Very fast
Martial arts training
Enhanced senses
Telekinesis
Absorbs/dissipates energy (see Revenge of the Sith to determine rate)
Uncontrolled clairvoyance
Telepathy (may require Force-sensitive receiver)
OPERATIONALIZATION
The next question is, "How do we get these two together?" Inter-universe travel, once a hallmark of the DC canon, nearly disappeared after the Crisis. And it is not known at all in the Star Wars Universe. The only answer, unfortunately, is there is no way to get these two together.
Unable to design an experiment pitting Anakin Skywalker against Superman, there is no way to tell who would win.
Thanks to mverta for the enlightening topic idea.