I've made a fluid simulation and it's working exactly how I want. I would like to save the simulation as a shape key-based animation, mostly so I can do another fluid simulation that interacts with the result of the first. I have the fluid cache backed up, so I can keep it separate from the second sim.
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It is not possible to convert a fluid simulation to shape keys. The fluid sim is in essence creating a new mesh every frame. Even though it looks like it is a mesh changing a tiny bit from frame to frame, it is not. Shape keys blend between two meshes that have the same vertex count, also they need to have the same vertex order, but they will technically still work even if the order is messed up. Since the vertex count from frame to frame changes you cannot convert a baked fluid simulation to shape keys.
Also you should simulate the two together as a single simulation because the results of one sim being simulated with interaction to another after the one is already simulated is not going to look very realistic anyway.
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$\begingroup$ Thanks for that. The first sim is an item melting and the second is the acid being sprayed on it, so for this project the two at once wouldn't suffice. That's ok. I'll try some other effects. $\endgroup$ Commented Mar 5, 2014 at 2:46
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$\begingroup$ Shape keys do require the mesh's topology do be constant. $\endgroup$– wcharginCommented Mar 5, 2014 at 4:17
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$\begingroup$ @BenJaguarMarshall It may be possible to fake it, see this post: blender.stackexchange.com/q/5328/599 $\endgroup$– gandalf3Commented Mar 6, 2014 at 23:16