What is the lowest latency communication method between a computer and a microcontroller?

Question

I have a project in which I need to have the lowest latency possible (in the 1-100 microseconds range at best) for a communication between a computer (Windows + Linux + MacOSX)

Answer 1

USB Raw HID with hacked 8KHz poll rate (125us poll interval) combined with Teensy 3.2 (or above). Mouse overclockers have achieved 8KHz poll rate with low USB jitter, and Teensy 3.2 (Arduino clone) is able to do 8KHz poll rate with a slightly modified USB FTDI driver on the PC side.

Barring this, and you need even better, you're now looking at PCI-Express parallel ports, to do lower-latency signalling via digital pins directly to pins on the parallel port. They must be true parallel ports, and not through a USB layer. DOS apps on gigahertz-level PCs were tested to get sub-1us ability (1.4Ghz Pentium IV) with parallel port pin signalling, but if you write a virtual device driver, you can probably get sub-100us within Windows.

Use raised priority & critical sections out of the wazoo, preferably a non-garbage-collected language, minimum background apps, and essentially consume 100% of a CPU core on your critical loop, and you can definitely reliably achieve <100us. Not 100% of the time, but certainly in the territory of five-nines (and probably even far better than that). If you can tolerate such aberrations.