The thermal energy from the accretion disk is due to tidal forces and friction. Matter falling into a black hole (or a neutron star or protostar, for that matter) is funneled into the accretion disk. As the infall/orbital velocity increases near the black hole, so does the friction within the disk. At the same time, the intense tidal forces near the black hole stretch the matter in the accretion disk, causing it to heat even more (Jupiter's moon Io is heated in a similar fashion, resulting in the solar system's most volcanically active object). The brightness increases, and increasing amounts of energy are released in the form of high-energy radiation, including x-rays.

Regular pulses from black holes (as opposed to neutron stars) are formed by clumps of matter separating from the inner edge of the accretion disk. It takes several orbits for a clump to finally fall to the event horizon, during which time the clump heats up even more than the accretion disk. The pulse frequency equals the orbital period of the clump around the black hole.

The brightness of the accretion disk can also vary irregularly as the rate of matter inflow changes. A black hole surrounded by plenty of matter will form a dense, bright accretion disk, while a "starving" black hole might have no accretion disk at all.
Source(s):
http://imagine.gsfc.nasa.gov/docs/ask_astro/answers/001106a.html
http://www.iop.org/EJ/article/1538-4357/468/1/L29/5291.pdf?request-id=402ec...
http://www.maineastro.com/alnitak/research/papers/black%20hole.pdf

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