Are the Borg really 'bad', from their point of view they are seeking perfection and helping everyone else by including them, I always thought the early Borg were great characters before they started to get watered down and certainly some of the scariest baddies, exactly because it wasn't emotion driving them but logic, all be it flawed logic from our point of view
As far as TV sci-fi goes aren't the baddest baddies usually 'The Government'?
I don't really know Dr Who or B5 but what about Stargate's Goa'uld? In some ways they seem badder then most who tend to have some justification, to themselves at least, for why their actions are either right or needed but the Goa'uld enslave and deceive billions simply so they can play god, knowing full well they aren't. That's just mean.