This is really cool! I do not have a 3D printer unfortunately, but have an interest in self-starting siphons that I have constructed with my kids using plastic tubing and empty seltzer bottles. I was wondering about the printing possibilities and it's good to see it confirmed.
I have had a design that I'm pretty sure would work (but have not even prototyped) for a binary ripple counter using a series of siphons. The units would not need to be devious or cup-shaped, but they should be stackable. The only difference is that the the outflow would be teed so half of it flows down to the next stage (an identical siphoned vessel) and half pours out the side into a central reservoir. For a fill volume (say 50ml) that starts the siphon, you would operate the counter by pouring half that (25ml) into the first (top) stage each time you want to increment the counter (the "clock speed" depends on the time to complete a flow). I believe that each stage would empty every second time it is filled by the previous stage (which only supplies half its volume), so the first stage would empty every other fill, the second every 4th fill, the third every 8th fill, etc. Each stage stores a bit (0 if empty, 1 if 25 ml). Since the stages are opaque (unfortunately), you would not be able to read the state of the counter easily, but could watch its outflow (which would only repeat every 2^n steps for n stages). Connecting the bottom reservoir to a recirculating pump with pulsed output of 25ml at appropriate time intervals might make an interesting fountain.