Atlas V (New Horizon's launcher) is hardly state of the art propulsive technology.
The best (with regard to delta-v) we have flight tested so far are ion thrusters. As a real-life example, NASA's Dawn spacecraft is expected to perform a velocity change of over 10 km/s entirely on its own over the course of its mission.
Assuming a one-ton spacecraft frame with two tons of Xenon propellant, using Deep Space 1 heritage electrostatic thrusters (de facto obsolete by now, but let's use them as a worst-case scenario demonstration). When you feed these figures into Tsiolkovsky's equation (dv = ve * ln((m_frame + m_propellant)/m_frame)) you'll get a delta-v capability of over 33 km/s.
A larger amount of propellant would of course increase this number, for example to 55 km/s with 5 tons of Xenon. This shows that there really isn't any upper limit on the achievable velocity (apart from special relativity of course). Only that at some point it becomes impractical to increase it, because the achievable delta-v grows logarithmically with respect to propellant mass fraction (i.e. even slower than linearly).
To find this threshold we need to define practicality. Let's assume that it's still practical for us (mainly economically) to have a spacecraft with a propellant mass fraction of 8 - that is 8 parts of propellant mass per 1 part of spacecraft and payload mass. Assuming we use the most propellant-efficient engine available today (that's actually being built, not one that is theoretically researched but not ready for deployment), Ad Astra's VASIMR with up to 30 000 seconds of Isp, we get (again, Tsiolkovsky) a delta-v capability of almost 650 km/s, or 0.22% c, or about 1850 years to reach the nearest star system. So that's what our current, state of the art and ready to fly practical velocity is, assuming the will power and finances exist to make it happen.
It has one drawback though - piss poor thrust levels. The 0.22% c VASIMR ship would have only 5 newtons of thrust available, which is perfectly OK for a deep space probe, but completely inadequate for intrasystem travel, or even manned flight.