...the Loom?
Personally, I think it's been a good while since Trek's last had so intimidating a villain to fight with. Watching the Loom just waltz through shields, forcefields, and even hull plating like they were nothing and being pretty much helpless to really do anything to do more than just slow them down was pretty nerve wracking.
You could barely fight them too. Phasers, even when attuned to the right frequencies, barely seemed to do anything to them. A volley of quantum torpedoes to the face at near pointblank range seemed to do more damage to the shuttle that fired them than to the single individual Loom they hit. Even Wesley Crusher, with all of his marvelous powers as Traveler, couldn't really do much to combat them, being of the opinion that the best way to fight them generally was to try NOT to if at all possible.
And that's all without getting into how they devour anyone and anything right out of history, a process that did NOT seem pleasant to experience, but even more horrifying is the thought it just completely and utterly wipes out the victim so thoroughly, it was as if they had never existed in the first place, with no records, no memories, no traces at all of them remaining. It's going to haunt me that Starfleet will probably never know for certain just how many they themselves lost fighting these guys.