Professor Zoom is able to move and travel at super human speeds. He can travel up to speeds of 7,500,000 mph., deliver hundreds of blows a second, walk on water, create cyclones and vibrate his molecules super fast to pass through solid objects.
Thawne can control his body at the molecular level, allowing him to vibrate his body through solid objects. While in this intangible state, he is able to breathe, but is immune to any airborne viruses. He is also able to vibrate so fast that light doesn't reflect off of him, rendering him invisible to the human eye. He retains sight even in this state.
Related to his super speed, Thawne is able to run in a circle and create a vortex. This vortex can be used for numerous purposes, such as pulling air out of the center to suffocate an enemy, levitating whatever is in the center, send a person in the center to another dimension, funnel toxic gases, and create a barrier, among other uses. He is also able to create tornado-like winds by spinning his arms quickly, and can use these to various effects, usually offensive.
Vast Superhuman Intelligence
At birth, Thawne was genetically modified to have an IQ of 167. Thawne's brain moves as fast as he does, meaning he is able to think extremely quickly. He is able to read a book at super speed, and retains this information in his short term memory just long enough to implement whatever he has learned. He is also a skilled forensic scientist. He is able to alter his perceptions in such a way that time appears to pass differently for him. In the span of a second he may have experienced years, and been able to alter elements of his environment while the time was passing, such as replacing a falling object or disarming an opponents weapon.
Eobard is also very intelligent and although not a very good fighter, Eobard uses his genius brain which can react and think at the speed of light, to his advantage.
Thawne no longer needs a cosmic treadmill to travel through time. He can do this as effortlessly as running down a city block.
Thawne can leech off "youth" and time from individuals to add to his own.
Thawne can transform into different stages of age appearance such as changing into a boy, or a senior citizen.
Thawne also learned to have the power to erase anyone from the timeline, removing all traces of that person's existence. He first tested this on Doug's friend, proving his "theory" worked.
When Eobard Thawne is experimenting with his new found powers, he goes to the past and freezes time at the exact spot before Barry get's struck by lightning, and freezes time in it's place.
Negative Speed Force Conduit
Eobard created his own Speed Force the same way Barry created the normal Speed Force. By duplicating the incident that granted the latter his powers, Professor Zoom was able to create his own Negative Speed Force by generating it through kinetic energy. Eobard can tap into it as normal speedsters can with the normal Speed Force and can apparently shut off their connection to the latter by "contaminating" it with negative energy. Through this, he has the ability to create multiple after images like Hunter Zolomon, the modern day Zoom, and can travel through and alter time (a feat which most speedsters were never capable of achieving).
Though not a skilled combatant, his brilliant mind led him to use his speed dangerously. Eobard has also shown to have supreme intelligence about the speed force/negative speed force, and can manipulate it effectively to his will.