Just a quick Q/note. Lets hypothetically say one
were to make something similar to a Roland AP7 Jet Phaser. This is one effect however is two distinctly different circuits. All on one board. The distortion part and the phaser part. Now, while it cannot be used as a stand alone distortion, there are modes for just clean phaser as well as dist + phase. Two very different sounding f/x in one unit. This is a bit of a "grey area". Is this considered two circuits or one? One or two entry fees? 
Hey Dave,
I will tell you this (and other judges... feel free to add or subtract from this)
What you are describing to ME is no different from someone entering anything from a TS with switchable clipping options -OR- even a Shin-Ei Fuzz/Wah clone.
Bottom Line = ALL ON ONE BOARD IS GOOD FOR ME!
Of course, if the judges MAJORITY decision is the other way, then what I just said is POOP!!! 
Dave,
You've brought up a valid point. In my opinion, the AP-7 is one effect. I understand your concern, seeing as how it combines different elements, but in this case, as Greg says, it's one effect.
Rule 4 states;
"4) Multi-board builds MUST contribute an entry fee for EACH board. The ONLY exceptions to this are charge pumps, 3PDT boards, and millennium bypass circuits."
But, if memory serves me correctly, didn't the AP series pedals also incorporated a noise gate of sorts on a seperate board? If that's the case, then I personally would have to go out on a limb here, and make the following judgement concerning the AP7 (and others, read further on);
If you build an AP7, as per the original factory layout, then I would accept the second board. Since the original configuration is such, then I would lump it into the charge pump, 3pdt board, mill BP, category.
Another good example is the Gemini III dual fuzz, where the circuit is comprised of two boards, piggybacked. Again, if one wishes to emulate the two board setup, it still counts as one effect.
I would apply this exception to any analog effect that was originally produced by the manufacturer as such (like the AP7, or Gemini III), and the burden of proof rests with the entrant. Just don't try selling us a fuzz circuit, and a delay, on two seperate boards, in one housing, as one effect. That won't fly, unless you can prove that it's a clone of a commercially available pedal (present or past) that has already existed in such a configuration. I reiterate, proof of such must be provided, or else we will insist on a fee per board.
That's my POV on the issue. If Jimi and Greg concur, then that should settle this issue.
Dino