Getting back to the square wave quest, today I took a bit of time from work (it is the weekend, you know), and I put a few pedals through their paces.
I did get to try both XO and '90s reissue Micro Synthesizers and Bass Micro Synthesizers from Electro-Harmonix. The older ones do have longer sustain. I didn't open the new ones, but I did use a Maxon CP9Pro+ compressor which was dimed on compression, and it cut out after 10 seconds. The reissues lasted for quite a bit longer.
I did try them with both active and passive pickups, but both with and without compression, there appeared to be no way to really keep the resonance in check outside of a small window. I don't want to have to try so hard for a particular sound, so all four of the boxes wound up, as far as I'm concerned, on the Shelf of Failure.
I also tried a variety of fuzz and overdrive pedals. The biggest happy surprise and crushing disappointment turned out to be the same pedal, the Ibanez PD7 Phat Head Bass Overdrive. The OD setting was pretty square, and sounded completely hollow running with a Boss CE-5 chorus. Feeding it with the Maxon felt completely square synth. Sadly, the pedal was extremely noisy when there was no signal. It might be great with a noise gate, but I'd rather look for a square wave which is quiet, instead of having to lengthen my signal chain.
The other pedal which was extremely nice for square wave fuzz, but disappointing, was the Behringer UF400 Ultimate Fuzz pedal. It sounds great with fuzz dimed and before chorus... but it has a monster high-pitched whine to it. I don't know which Boss pedal this is based on, but I think I want to try it and see if the situation is a bit quieter. If the Behringer hadn't had a whine to it, I'd have bought it on the spot. Could there be variations between them, and would patience have been rewarded? Maybe, and I might try that later this week... but there's no way I'm going to search the Internet for the best price and get stuck with a unit with that noise.
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One pedal which (for whatever reason, marketing hype or whatever) gets touted for square wave goodness is the Zvex Mastotron. Perhaps this is true for some particular set-up, but I've not managed to get a square wave out of it. I'm a huge fan of the Mastotron, and it does sound synthy, but considering I was specifically searching for "square wave pedal" on Google, and kept running across the Mastotron, I think it's worth noting in at least one place that it falls short in the "square" department.
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So far, the only pedals I've personally tested, and which have managed to do a decent square wave without noise have been the SYB-3, SYB-5 (and its clone, the Behringer BSY600) and the Pigtronix Mothership. All of them are triggered oscillators, instead of circuits which clip off a sine wave, like the Behringer UF400 and Ibanez PD7 already noted. It makes sense that an actual oscillator would sound better, and with less extraneous noise, than a clipping circuit.
There is one clipping fuzz which seems to sound great in every sound sample I've run across, so I've decided to pick up a Chunk Systems Brown Dog gated bass fuzz pedal. It's also possible that there's some square-clipping fuzz I haven't tried yet (like the Boss version of the UF400) which will do what I'm looking for on the cheap. I'm starting to doubt it, though.
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Really, having been trying all these pedals out just makes me wish the Markbass Super Synth did square waves. *sigh* It already tracks so well, and square would have made it that much more perfect....
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Regarding everything I just wrote, keep in mind that these are my own experiences, running with my own instruments and signal chain. Your experience may vary, but hopefully someone will find these observations at least mildly helpful.