Large slow speeds (Sulzers, B&W's, etc.) will burn a mixture of oils without too much negative side effects, up to a point. The amount generated aboard ship isn't likely to cause much harm to the fuel/exhaust systems. Hydraulic fluid in large quantities should be avoided because of the slag it will create in the head and exhaust system. We've burned it in auxilliary boilers in the past, though (mixed with diesel, to support combustion).
Shoreside waste disposal companies send the processed waste oil to steam plants and marine fuel suppliers for mixing with bunker C.
I would definitely avoid using anything like this in an EMD or any other engine that's designed for using light fuels, though.
If you do burn it, you'd want to add it to the deep tanks just prior to fueling in order to disperse it better. Distribute it evenly to each of the tanks being filled.
There's the potential for parafinic precipitation due to mixing oils from different base stocks, but the relatively small quantities you'd add to your base fuel shouldn't cause this to happen.