My daughter just finished a similar project.  She had the idea to use gel wax as the cytoplasm.  So I bought the wax at craft store, melted it in an old bean can, slowly, using a chopstick to stir so I could throw the can and stick away later.  As soon as it was melted, I poured it into a styrafoam soup bowl.  After about 15 minutes or so, it was ready for the other parts to be added.
 
My daughter used things like a golf ball, candy, beads and folded paper to represent the different cell parts.  When the wax was cooling and thickened, these "parts" stayed close to the surface and were easy to label.
 
When the wax was completely cool, she cut away the rim of the soup bowl and voila, she had an animal cell.