Cylon vs Borg?
Borg are simple but effective. They assimilate and integrate the conquered into the Hive mind. They are ruthless but they lack motivation. Their only reason for existing is... because they exist. They are not more complicated than a bacteria who adapts, survives, replicates. They are the virus of the Universe. But they are weak... one one hand their programming is limited, they cannot create anything new, on the other their organic bodies are more of a nuisance. Voyager took great pains to turn them into something more interesting but their end is fitting. They are something less than "human".
Cylons? They are the best part of Battlestar Gallactica. One one hand you have the humanoid clones. I found these to be boring, confusing and limited as a concept. They are the greatest weakness of the Cylon, something made up for TV purposes only. I don't want to go into details, lest I spoil the fun. The fleshy robots? Now we're talking. Their ability to reincarnate (The Prestige style, with all the bad implications) makes them unique and highly fascinating. The episode SCAR from the second season is the only time we see this in action to it's full extent. It's my favorite episode of the show as it says so much about them. They still act as individuals and overcome their limitations. They have a motivation, other than killing humans. They are a religious bunch, trying to figure out what they are meant to do. In other words, they are more than "robots". They have free will and a sense of freedom.
So while Borgs are by nature a bad concept and are doomed to eventually fail, the Cylons have the tools to become something amazing. But Cylons are not something to be feared, as they also lack most of our human weaknesses. Cylons are creators, not destroyers. It's nice to imagine what they would've done on their own (without the war with humans), but I guess they would've turned into a benign race of explorers.
So what would be the greatest threat for us? By far, The Matrix. Watch Animatrix (The Second Renaissance) and you will probably come to agree with me. Yes, it's the old "Terminator" idea, but the story twist with the human batteries locked in a virtual existence is more then enough to make you believe it could actually already be true