I'm calculating efficiency this way: deltaV/fuel mass. How much km/s you can get from a tonne of propellant (on average, ignoring the fact that the last ton of propellant gives you quite more deltav since you don't have to accelerate that much propellant when you are using the last drops).
Thrust isn't really relevant here in my opinion, since it doesn't matter how much time you need to reach a given velocity in most cases. It would count if you are able to accelerate until midpoint of the trip though.
My calculations:
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Efficiencies: (full, empty)
Xylophyis: 756, 1880
Lunar shuttle: 94, 164
Pumpkinseed: 987, 2274
Amphiesma: 326, 776
MolaMola: 141, 404
Sinonatrix: 217, 458
Kanara_civ: 150, 267
Natrix: 52, 142
Wave: 244, 585
Deneb: 52, 157
VentureStar: 24, 67
DSMiner: 2, 9
Nerodia: 5, 25
Malabar: 3, 9
Vatakara: 3, 9