They were used to show Team Rocket's control over their minds.
As far as game mechanics go, the Dark prefix is counted as their name (so you could have 4 Kadabra and 4 Dark Kadabra in your deck, but still only 4 Abra). They get the bonus for Darkness Energy, even if they aren't Darkness type (old Dark Crobat for example), but they don't get double bonus if they are Darkness (example, Dark Tyranitar would only get +10 and not +20 for being Darkness and having Dark in its name).
Since Dark is part of their name, you can't evolve them into normal Pokemon (Dark Kadabra could not evolve into Alakazam because Alakazam evolves from "Kadabra," not "Dark Kadabra."
Not sure what else could go here... hope this helps.