fission powered ion thruster is probably the most useful, if you can produce a compact (and most importantly!), lightweight fission reactor to couple it with. (The thrust provided by an ion engine is very small-- Less than 1 newton, IIRC. However, the propellant consumption is very small, compared to the delta V it produces, especially over the lifetime of the engine, since it can do continuous fire, potentially for years at a time.)
Say for instance, if you have well calculated rendezvous of a large transport of some kind (Hello early Bungee title, I am borrowing the Marathon for this example), this heavy vehicle could use a combination of deployable solar sails and ion thrusters to keep its velocity high, then enter and leave high orbits of target bodies in the solar system after getting local reaction-mass replenished (or if using only the ion thruster/sails to do the orbital maneuvers, use a long transfer trajectory.) It would have to operate on a *VERY* strict time-table to keep favorable rendezvous going, but it could be used to ferry large amounts of material/people around the solar system. It is important to note that this vehicle does not EVER slow down. Once it gets up to speed, its engines are ALWAYS hot. The most it does is enter a capture trajectory for a high orbit capture, with controlled burns to accomplish this. It would then burn its engines and selectively deploy and retract its solar sails to do oberth like operations to exit orbit, and breakaway, based on its timetable. Its high velocity means it has to assume a high orbit.
Remember, a heavy reactor in space is always bad. It means you either can transport less cargo, or will be expending more energy for a gain in delta-V for the energy expended, in a very unpleasant curve with ever increasing diminishing returns, as the reactor gets heavier. Lighter reactors will always be preferred, even with a super-transport like the Marathon.
If being used inside a star system like this, expelling the waste out the tailpipe is not advisable; the waste products could be vastly more useful in space as the power cell inside RTGs for deployed robots and probes. The reactor's waste should be transferred to local port authorities for that use.
@Eric Blank, RE: Port authority
Remember, aliens are likely to be either waaaaaaaaaaaay more advanced than us, or waaaaaaaaay less advanced than us. Only seeing the "way less advanced" point of view is dangerous. You dont want to show up in orbit of Aiur with a nuke smoldering rustbucket, and have to fart out a bunch of radioactive polonium. The protoss will take exception, and it wont end well for you.