Mana Manipulation and Energy Control
In What Are Little Girls Made Of?, Gwen's magical powers are revealed to be of alien descent inherited from her grandmother Verdona, a member of a free-spirited alien race of pure energy beings known as Anodites, from the planet Anodyne. Verdona tells Gwen that, like herself, Gwen is also an Anodite; she has "the spark" and thus is able to freely manipulate and control mana.
Gwen can create energy blasts, shields and barriers. Her powers are mainly used like energy constructs, allowing her to make many different types of structures like, hammers, protective helmets, battering rams, beams to grab and throw enemies, stepping stones/platforms to carry her and others though air, safety nets; it also turns out Gwen can also synchronize her martial arts styles with her energy manipulation abilities.
Gwen has more mana-related powers: She can find any person she wants by detecting the traces of mana that he/she left. She can also absorb mana.
She also has the abilities of telekinesis, teleportation, heat vision, telepathy and healing living beings. She can also transform into an Anodite. In her Anodite form her powers are greatly enhanced, having demonstrated the abilities of flight and size alteration.
Magic and Spells
Gwen is seen using magic through casting magical, mystical spells, and reciting spoken incantations thus enabling her to use various magical powers and abilities.
In the original series all of Gwen's spells are said out loud to activate her magical powers and abilities, but in Ben 10: Alien Force, most of her spells are used non-verbally.
On two occasions, Gwen used the five mystical Charms of Bezel to become a super heroine by the name of Lucky Girl. At first her power and ability drew from the luck-granting Charm of Bezel, which innately gave her complete and perfect luck in everything she did. While wearing the charm, any action she took would result in a chain reaction benefiting her original intent, but usually injuring Ben in the process. She later brought back her superhero identity in the episode Tough Luck after obtaining the legendary lost Keystone of Bezel, which greatly increased her natural abilities to superhuman levels rather than just affecting her luck. Both times, Gwen was forced to retire when the five Charms and Keystone of Bezel were destroyed.
In Where the Magic Happens, Gwen claims that being self-taught in magic is not so easy as it looks. Trying to get into Yahwahtacsip she mistakes its name for "Wah Di Tah", saying that she knows how to read it but not pronounce it correctly.
From Map of Infinity onwards Gwen begins to cast spells and recite spoken incantations again. Gwen is less knowledgeable than Charmcaster and Hex, having been self taught, but she is also more powerful than Charmcaster until Charmcaster obtained the Alpha Rune, after which she was powerful enough to defeat Gwen with ease.
She has also learned to astral project through magic.
Athletics and Martial Arts
Gwen is a capable gymnast and martial artist. Even in the original series, she was occasionally shown to be quite good in hand-to-hand combat fights against enemies who had normal strength levels. At the age of fifteen it is revealed that she has already received a black belt in taekwondo.
When preferring to use her athletics during fights or when she cannot rely on her magical and Anodite powers, she is shown to be highly skilled in hand-to-hand combat.
According to Dwayne McDuffie on one of his forums, Gwen does martial arts, horseback riding, softball, skiing and cross country. Turns out that Gwen can also synchronize her martial arts styles with her mana manipulating abilities. In the episode Ben 10,000 Returns, Gwen is shown creating a whip of mana energy and using it as a weapon along with her fighting skills. When Kevin asks her how she learned it, she states remembering it from an old movie.
Knowledge and Intelligence
Gwen is shown to be very intelligent and knowledgeable. Before discovering her dormant innate magical and Anodite powers, she would often use her superior intellect to help Ben. She is shown to be a bit of computer and tech wiz as well. She has her own laptop which she uses to research enemies she meets.
In Back With a Vengeance, Gwen switched the Omnitrix with a bomb, saving both Ben and the world, showing her cleverness.