I’m using RetroArch-Phoenix and RetroArch on an x86_64 Ubuntu Linux laptop, with all the cores that libretro-super provides; I’ve compiled everything myself from source.
Currently the RetroArch-Phoenix GUI has the ability to configure analog controls, but joysticks don’t work in-game with RetroArch because there’s no “analog button” to switch to/from analog mode. Regular Mednafen has the button available, and when the button is pressed an on-screen message appears indicating analog mode has been turned on/off. I don’t know how support for an “analog button” could be added, but adding support is required for games like Ape Escape to be playable. I can still use regular Mednafen to play games with joysticks, though.
Edit: Nevermind, I found the “DualAnalog” option in RetroArch-Phoenix’s menu entry Settings->Controllers->Port 1->DualAnalog; setting the option makes joysticks work in the Mednafen PSX core.