Not an easy question (Klingons vs. Cylons) because they exist at pretty different tech levels. There aren't any energy-beam weapons in Galactica, so I don't think the Cylon ships would have any defense against disruptors, leading to a quick Klingon victory and much bad Opera.

Give them equal tech, however, and the Cylon's superior strategic capability comes into play. Cool dispassionate machines with a hive-mind vs. berzerker warriors who advance through assasination? My money's on the Cylon and G-d's plan.

But what would the Borg do with the Cylons, other than assimilate some really good-looking blond or asiatic androids? What would one do against a cube loaded with a million hot blonds, who could experience each others orgasms simultaneously?

I suppose one could draw some parallels in the season finale: there are the continue the mission crowd who want to go to Earth and don't believe the Cylons are anything but evil (the Bush crowd with the continuing GWOT) vs. the let's stay on this new planet, we are exhausted by war (the anti-GWOT crowd). The Bush crowd types did engage in some bad actions -- mistreatment of prisoners, attempts to steal an election; but the anti-GWOT crowd doesn't/is unwilling to see the threat posed by the Cylons.
Of course the parallels aren't perfect, Cylons are not so much Islamist terrorists as they are humanity's creation and both sides will eventually have to reconcile with each other.

And I'd pick the Klingons. The Cylons have no beef with them and wouldn't necessarily be willing to die to get rid of them while the Klingons are a warrior culture. Just don't have and herbal tea drinkin', tai-chi doin', new agey Worfs on board.