Prisoners are only useful once and only when you have them as captives on board a ship, from there you can drop them off at any colony you wish. Once at a colony they will open up a new research project that will allow you to see the full racial details regarding species tolerances for the race they belong to, after that they just sit as prisoners on the colony and do nothing more.
The way it works though can leave you with some problems from an RP standpoint, if you have a colony set up as a your main research base or you happen to keep all of your research on your homeworld. You now have the issue of also suddenly having prison camps and the like on those worlds, personally I prefer to create specific penal colonies where all prisoners are unloaded too. Since the cost for the race project is only 5000rp then you can normally get away with just keeping a small number of research facilities there for that project alone.
But you do need to think carefully before unloading prisoners to any colony as once they are there that is where they will stay forever. You cannot move them by any means and the only thing that will remove them is the removal of the colony itself. Think of them sort of like a team but unable to be picked up, they sit outside the normal things that effect the general population such as colony cost, radiation etc. I generally have a habit of creating a penal colony on the closest object to a gas giant with a large amount of sorium, that way my fuel harvesters choose that colony as a place to dump fuel off to. Who doesn't want a piece of cold dark real estate as a dilithium mine with prison labour?
