My husb. and I produce hands-on science labs, and you can find two completely free labs at our website that compare plants and/or seed sprouting in various ways.
Compare how different environments (in one small jar) encourage or discourage the sprouting of radish seeds. Other seeds could be substituted, but radishes sprout really quickly, so you can see the results right away:
http://topscience.org/books/radishes38.html
Compare different plant types by growing a monocot (a popcorn seed) and a dicot (a pinto bean seed) in the same small jar. Keep a journal with drawings comparing the growth patterns:
http://topscience.org/books/corn_beans39.html
If those don't capture his interest, there are four dozen free activities, many of which involve comparisons, of different length pendulums, of the transmission of heat, of electrical conductors and insulators, and much more. Go crazy!
UPDATE: As I think about your questions, it sounds like your son is possibly supposed to compare different commercial products? If that's the case, comparing paper towels probably won't yield much difference, so I'd go with the planting mix. If you wanted, you could compare some of the many soilless mixes currently available as your variable.
I'm a little doubtful, based on my years of gardening, that you'll get much difference watering with those different drinks, other than some plants would possibly not survive as long as others. All of the drinks are sugary, possibly acidic to various degrees, and could clog the plants' ability to take up nutrients.
If you were to compare three different types of liquid products, like tea, pop, and flavored water (or perhaps vitamin water, plain water, and a carbonated water), you might get measurably different outcomes. My dangling question would be, however, would the results be meaningful or relevant to a real-life situation?
One last suggestion, if you're growing any plant from seed, individual sprouts will be widely variable in size and vigor. So it would be a good idea to have three or more seedlings in each test group, so you can average the results.
Good luck. I think it's really neat that your son gets to design an experiment and practice the scientific method.