I work downtown and get to work fairly early. One of the best places starts serving at 6:30 and that's City View Cafe. Located at 1300 Fannin on the 13th Floor. You can get a hot breakfast for under $3.00.
Also, Alonti Deli located in the tunnel under the Center Point Energy Building serves made-to-order omelets. I am not sure about the price, but for the amount of ingredients, and the taste it's worth it.