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They recently changed the Nexus machines on the US Customs side (well recent as in the last year or so), so that you MUST use your passport. Prior to that, the older machines didn't require you to actually place your NEXUS card or passport on the machine and relied solely on your iris scan.
Coming back into Canada, you need your card but they don't ask for your passport. That too seems like something fairly new (also within the last year) as we used to just do iris scan there too. Also, if you're coming in late at night, sometimes the NEXUS terminals are offline and you'll have to get into the regular line. It'll be a lot faster if you have your passport so you can use the automated booths there as well. (I'm hoping though that the manned booths can process a NEXUS card though)
Never tried the Global Entry at US airports yet. I'd suspect you'd need passport for that though.
Clear is actually something else and doesn't have to do with crossing any borders. It's just an "express line" for the security checkpoints at US airports. Probably only useful if you live in the US and frequently fly domestically.
Most airports without any NEXUS facilities won't take the NEXUS card as a form of ID. (for example, I couldn't use it at BLI to pass security) Always bring it when you fly.
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