I've listed some references below. The most useful general review paper is Adams 1997, except that it predates the discovery of dark energy.

> Will there be a day that the universe becomes completly dark when all the stars burn out?

Yes. The hydrogen fuel burned by main-sequence stars only decreases over time and is never replenished. Some hydrogen will end up permanently unavailable to star formation, e.g., in gas giants. The last stars to burn will probably be very small, dim, "frozen stars" that can exist only because of the high proportion of heavy elements (Adams, p. 8). By $10^{14}$ years from now (possibly sooner), all star formation will have ceased and all stars will have evolved into degenerate objects (Adams, p. 9).

> Does all the cooled bodies eventually collide due to gravitational forces?

No. Gravity doesn't typically make things collide, it makes them orbit each other. On time scales of $10^{19}$ yr, most stars will be ejected from the galaxy (Adams, p. 12). A minority of them will not be ejected and may either undergo random collisions (with a time scale of $10^{22}$ yr for brown dwarfs, or much longer for degenerate stars) or gradually migrate toward the galactic core on time scales of $10^{24}$ yr due to dissipation of energy into gravitational waves (Adams, p. 13). In the end, about 1-10% of stars will end up eaten by the central black hole, while the rest escape the galaxy (Adams, p. 17).

> Will black holes eventually dominate the universe?

No. As described above, most stars end up as brown dwarfs, white dwarfs, or neutron stars, which are ejected from their galaxies. Due to some counterintuitive thermodynamics, they are probably eventually spontaneously ionized (Baez 2004). This supplies a population of unbound massive particles, which adds in to the population of such particles that simply never happened to undergo gravitational collapse into a macroscopic body. (If proton decay exists, then it modifies this picture somewhat, e.g., neutron stars evolve in certain ways, but the end result should be the same.)

In addition to these particles, we have a population of black holes. On sufficiently long time-scales, these evaporate into a variety of particles, the most numerous of which are photons (but *every* possible type of particle is created by Hawking radiation).

So we now have a universe whose only inhabitants are various individual particles: photons plus massive particles. As the universe expands by a scale factor $a$, the mass-energy density due to photons falls off as $a^{-4}$, while the mass-energy density due to material particles goes like $a^{-3}$. The differece in exponents is because photons get cosmologically red-shifted. This will cause the photons to eventually become a negligible component in terms of their contribution to the mass-energy density.

Accelerating cosmological expansion causes the massive particles (probably mostly dark dark matter, neutrinos, and electrons and positrons) to end up within their own cosmological horizons, so they can no longer interact.

Adams and Laughlin, "A Dying Universe: The Long Term Fate and Evolution of Astrophysical Objects," 1997, http://arxiv.org/abs/astro-ph/9701131

Baez, J., 2004, "The End of the Universe.", http://math.ucr.edu/home/baez/end.html

Dyson, Time without end: Physics and biology in an open universe, Reviews of Modern Physics 51 (1979), pp. 447–460, doi:10.1103/RevModPhys.51.447.

Freese and Kinney, 2002, The ultimate fate of life in an accelerating universe, http://www.arxiv.org/abs/astro-ph/0205279

Hu, Hawking radiation from the cosmological horizon in a FRW universe, http://arxiv.org/abs/1007.4044 

Krauss and Starkman, 1999, Life, The Universe, and Nothing: Life and Death in an Ever-Expanding Universe, http://arxiv.org/abs/astro-ph/9902189