First off, nanomachines. My basic idea for this is little factory nodes scattered here and there in a system. They don't attack you unless you get to close, but when you do, you're ambushed by a horde of tiny ships the size of a flenser shot. When they fire, there's an explosion behind them, and they fling themselves at your shields in a rather violent manner. If you can manage to get through to the factory node without being knocked back, you can turn it off. Or you can just blow it up. That'd be much easier. Less valuable, though.
These nanofactories would try to prevent anyone getting within, say, one sensor screen's worth of them. (don't even ask what that is in LS

Secondly, Microsingularities. Specifically, the Quasi-Sentient Microsingularity Cannon (the microsingularities are quasi-sentient, not the cannon). This would launch five to ten fast moving little black dots; these would ideally be ships ordered to patrol a certain area of space relative to where they were fired. These little ships would have a 'ramming' style weapon. When a ship entered their area of space, they would start popping through it, in and out, until it was destroyed. Obviously the player would want to steer clear of this.
Not sure exactly why those ideas came up. Blame not being able to sleep. They might be better suited to post-1.0.