I run on EMU (when i choose to run this game) and my controller of choice is the DualShock 3 (PS3) controller, however for console i would say the best controller to use would be the GBA SP due to the buttons. I find the SP buttons are easier for mashing and precise inputs which in my opinion the GC controller does not provide for this game.

Most runners that run on console use the GBA SP as a controller.

I own a hori GBP controller and personally, I much prefer using the SP. This is mainly due to the directions on the d-pad being more discrete. Your mileage may vary, and I'm sure it's possible to use the hori pad successfully, but that's my experience.

I personnaly use the GBA SP because the Dpad is way more precise than the GC joysticks if you run on GB Player, there is to much dead zone.