what about the jets of particles that shoot out from black holes when their anti particle is pulled over the event horizon? will the universe just be filled with a pile of particles floating around? also, what happens to matter in a black hole? does it simply disappear, squashed into nothingness?
I've never heard of the jets being caused by anti-particles. Our universe is pretty much exclusively matter so there are no anti-particles around! The jets are a result of the conservation of angular momentum. These should ensure that not all matter is swallowed up but there would be very little left and it would not be dense enough to form stars or galaxies.
The matter in a black hole does not cease to exist. If it did then a black hole would not have the huge gravity that it does. Over time matter actually leaks out of a black hole via a form of quantum tunneling called Hawking Radiation. So, in effect blackholes evaporate over billions of years.
Now, as to what happens in the longer term it all comes down to the rate of expansion of the universe. If there is enough matter in the universe all the black holes will get pulled into each other and reverse the expansion of the universe and basically cause a 'big crunch', if on the other hand there is not enough matter in the universe to slow and reverse the expansion then the universe will expand so rapidly that the stuff that evaporates from the blackholes will be spread out so thinly that the whole universe will essentially become empty. The latter is what current measurements of the expansion seem to be implying.
  