How about a converted, obselete destroyer, such as a Typhon, for use as a colony ship. It prabaly in combat condition has a crew of 10,000, and if all of the combat systems were romoved (on the principle that they are old, buggy and not suitable for upgrade), this could be significantly increased. If the colonists were put into cryotubes, this could be increased further. remeber a colony ship does not have to be big as many colony types would have small popuations (I would expect a mine on an airless rock to have a population of less than 1,000). As for the use of Babylon 5 ships, I think I understand shiv_pa's point. While the combat vessels of course would be completely unsuitable, the liners would make ideal colony ships.
I have been trying to put together a small camaign about setting upa major colony, using the method I described above, but I cannot work out how to get something as valuable and vulnerable as a colony ship into a combat zone to have some missions.