blight has just released version 0.0.8 of his SDL input plugin for Linux N64 emulators. Some words from the author:

I just installed 2.6.0-test4 and my gamepad... The problem which disabled analog axis was enabling keyboard at the same time with the joystick so that the keyboard state was the preferred one and the axis state was overwritten... this is also true now, but only if a key is pressed, else the analog axis value is used

Sounds good, keep up the good work blight!

Download both the binary and the source from our downloads section.