Unfortunately there seems to be no deadzone option similar to the one in standalone mupen64plus, so I had no option but using xboxdrv.

The good news is, xboxdrv is not that hard to use if you follow mediamogul's excellent Advanced Controller Mapping Guide.

After a few tries I had a working base configuration, but the joystick output was still too low. After mediamogul's suggestion and some trial and error I got a configuration which works really nice for me (real N64 Controller and HuiJia USB GamePad adapter). What's nice about xboxdrv is, that you are able to rename your controller, which makes keeping track of multiple controllers with the same name quite easy.

This is my configuration:

sudo /opt/retropie/supplementary/xboxdrv/bin/xboxdrv \ --evdev /dev/input/event2 \ --silent \ --detach-kernel-driver \ --force-feedback \ --deadzone-trigger 15% \ --deadzone 15% \ --device-name "N64 Player 1" \ --evdev-absmap ABS_X=x1,ABS_Y=y1,ABS_RZ=x2,ABS_Z=y2,ABS_HAT0X=dpad_x,ABS_HAT0Y=dpad_y \ --evdev-keymap BTN_THUMB=a,BTN_THUMB2=b,BTN_BASE=lb,BTN_BASE2=rb,BTN_BASE3=tl,BTN_BASE4=start \ --ui-axismap lt=void,rt=void \ --ui-buttonmap tr=void,guide=void,back=void,x=void,y=void \ --calibration x1=-16384:0:16384,y1=-16384:0:16384 \

I hope this helps if someone else has trouble using real Nintendo 64 controllers!