I like races from before time. The ones that have been around twice as long as we have.
Huedocan: A race of beings who live in a Dyson Sphere. They use crystalline technology (Stargate Tech), Disruptors, matter manipulation and matter storage devices. All powered by the electromagnetic field around your body and control by psionics.
Keracan: Massive machine which amplifies Psionics (Think magic.) on a world wide scale.
Shadox: (Fred Saberhagen's Berserkers series with an organic twist). Beings that are organic metal and hate other lifeforms. They are lurking out there somewhere.
These are just the one's I'm willing to talk about. I've made several of these races for different stories over the last 40 years. Hell, and some of them are just sophonts that look at us in a different way. I've got a big write up in my files about the Saurian Question. Simply put; Would you give a more primitive race advance technology? Another way to put it: Would you give a 5 year old a load gun to play with while, you stand there and watch him/her? He/she may not know how to use it or fire it, but there is that chance, he/her could fire rounds off accidentally. Which might or might not kill, you or themselves? In any case, you are now the evil threat to the planet because you gave them the tech do destroy you or themselves.
Truly any race above your tech level could seen a a threat and the Saurian Question. I don't do the Star Trek "Prime Directive' in this case. (forget the character name?) The Admiral's solution (In the beginning of 'Mote in the Eye of God' by Larry Niven's) nuke the crap out of them or corridor off the world from the rest of the interstellar communities until they grow up! Those are truly the only options in my universe.
SO they really don't have to be a big scary super aliens to cause havoc, they just got to reverse engineer the stuff at Area 51 and piss off their stellar neighbors.