Captain Marvel has super-strength. His strength level, which can be enhanced by focusing energies of his nega-bands inwards, may be anywhere from class 15 to class 50.

Power Source: Both Physical ability and Negabands.

Captain Marvel can  fly and travel at high speeds, even in outerspace. He can breathe in environments that contain no oxygen. (However, he cannot breathe in water, because there is oxygen -- and he just can't extract it, as seen in Captain Marvel #2)

Power Source: Negabands.

"Flight"

"Cosmic Awareness" is the power to be cosmically aware of his surroundings. Right now, Rick and CM have no little control over the Cosmic Awareness, and it is contantly on.

Power Source: Physical ability

"Cosmic Awareness"

Captain Marvel can fire beams of Photon energy from his nega-bands. PAD also said at the Captain Marvel Message Board: "My feeling is that the energy he funnels through his negabands can be used in a variety of ways. He can direct it internally, giving him accelerated strength. Or he can manipulate it to form the equivalent of energy "shields" to give him some insulation against attack. Think of it as cosmic shock absorbers. If Marvel was just standing there, offering no defense, and the Hulk hit him, they'd be picking up the pieces from here to Saskatoon. As it is, in a fight he was able--through quick action with the negabands--to deflect/absorb some of the impact. Some, but not all."

Power Source: Negabands

"Photon Blasts"

Rick Jones uses the negabands to switch place with Captain Marvel by slamming them together and he is replaced by Genis-Vell (Captain Marvel).
The nega-bands also are like a funnel of energy, giving Marvel a lot of his un-natural powers.
In Captain Marvel #3, Genis (while Rick was in the realworld) was able to cause the negabands to release a powerful Jolt of energy. However, Rick Jones cannot tap into the Negabands full energy potential, but can release energy Jolts into someone if they come in contact witht he bands.

More on How Rick and Genis Were Merged

Power Source: Negabands

"Exchange"

"Energy Jolt"

The "Exchange"

Rick Jones and Captain Marvel are molecularly bonded. Rick switches places with him using the Negabands. When one of them is in the real world, the other will be in a "nullfield" which protects them and keeps them immoble. This nullfield is found in the microverse. In Captain Marvel #4 & #5, Captain Marvel broke the nullfield when he transported Drax to the microverse with him, so while one is on Earth the other is free to roam the Microverse. And they fell to the alien planet K'ai. This is where Hulk first met his green-skinned alien lover, Jarella.

Power Source: Negabands, and the fact that Rick Jones and Captain Marvel are "missing" Atoms, and they need to be connection to survive.

"Nullfield"

Mental Connection

Rick can speak to Captain Marvel (and vice versa) via some unknown mental connection, and they see each other's reflections instead of their own.

In Captain Marvel #15, Captain Marvel was able to concentrate and "enter" into Rick's dream, and wake him up by mentally creating an image of him banging symbols together. This leads to suggest their mental connection may be closer than previously thought. Whether through concentration Rick can do this as well, or this ability is uniquely Genis' remains to be seen.

Power Source: Physical Ability

"Dream Invader."

Spatial Aperture

Genis at one point was able to create spatial apertures with his nega-bands. It's a hole between the universe and the nega-verse, it kept whatever was trapped in the aperture in a stasis field. Unable to move, but able to talk and listen. Since Genis' connection to the negative Zone is seemingly gone(to what degree, I do not know) it is unclear if he still has this ability.

Power Source: Negabands.

Energy-to-Mass Conversion

This isn't exactly a power of his. In Captain Marvel #16, a freak accident causes Captain Marvel to turn into living energy, and using his Nega-Bands he was able to reform himself. However, he cannot do this naturally himself, or at least not yet, maybe eventually when he learns more about his powers.

Power Source: Both Physical ability and Negabands.