I M Ready's theory looks good.
HFuel is the cleanest fuel around, as Hydrogen when burned just produces water. Nuclear reactions using Plutonium and MOX are likely to lead to some emissions of nuclear waste.
Oxidisation of Deuterium is likely to lead to water emissions only, too, but would be less economical than H-fuel. (Higher density, so higher mass per energy released). However, impulse type engines would be better on Deuterium, as more mass (Deut >hydrogen) would mean a higher resultant opposing force when the fuel is pushed out of the engine, making it more effective for propelling it forward.
I believe heavy water (Deuterium Oxide) can be used in Nuclear reactions, but don't know enough about it.
It might also be noted that Light is, essentially, wasted energy, so the brighter a ships' trail, the less efficient it's engines are. However, I doubt Freelancer accepts this concept.
Also, it should be noted that energy release may not be the concept these engines work on. Impulse-based engines rely on pushing material out of the ship in order to propel it forward (like the recoil of a gun, or an ice-skater pushing on another ice-skater, and both of them moving in opposite directions).
I think we have to be careful applying scientific principles to freelancer, as it largely ignores all reality, arguably making it more fun.
"Burning" engines aren't going to be that helpful in space. there's no sound in space, and also nothing to push against.