As we have just seen, Harrison Wells is indeed the Man in yellow, the Reverse-Flash; PROFESSOR ZOOM!!!

But the real question remains as to who he truly is, and I have compiled some theories as to who he may be:

Eddie Thawne: my supporting evidence for this being that out of all the police officers he attacked, Reverse-Flash did not strike him for some reason. Giving the slowly growing animosity shown between Barry and Eddie, this may start the Allen-Thawne rivalry that we've seen in the Flash comics. 

Eddie Thawne's son or grandson: given the fact that the Flash deals with a lot of time travel orriented stories, Harrison Wells may just be his son or grandson with the same shared animosity they had toward the Flashes for centuries. Given that Professor Zoom is cold calculating and a high functioning sociopath, which Harrison also is, he may be doing all of these things with Barry to ensure the rivalry or some other agenda. Not to mention in an earlier episode; Eddie mentions being the son of a politician. This may give some sort of identity as a relative of Professor Zoom, Thaddeus Thawne, is the president of Earth, or simply subtly hinting at things. Another hint about this is how Harrison mentions how he felt that the particle accelerator's completion felt like a century to complete, implying some time travel and possibly implementing futuristic tech, as Barry says that his work is ahead of his time. 

Max Mercury or Johnny Quick: There is not a lot of speculation about this theory other than the fact that Harrison states that the particle accelerator ruptured a dimensional barrier. I know that Johnny Quick may be a plausible theory, given the fact that he's an alternate demented evil version of Barry Allen. Max Mercury is a potential theory, as they subtly referred to him in the latest episode; Mercury Labs. GIven how Harrison is providing Barry advice and counsel like how Max did with Wally West, there is a very slight possability that Harrison Wells is a demented alternate dimensional version of him.