How does the Nintendo 64 detect a controller is connected?
It turns out I wasn't sampling the GPIO long enough. I wrote a little Raspberry PI kernel module to sample the GPIO as fast as possible for 3 seconds, and record a semi-accurate trace. Here's what showed up on the wire after one second:



In summary, the N64 waits one second after boot to ask the controllers to identify themselves with 0x00 followed by a stop bit.

Thanks Chris Stratton for your help!