I use the Micomsoft/Sharp Cyberstick which was created by the President of Micomsoft who was a huge Afterburner fan and wanted proper controls at home. The XE-1AP hand-held controller also works. But for PCE you need the XHE-3 adapter which is much rarer then the actual controllers. Using the full size stick with FW takes some time getting used to, but after proper calibration and a little practice it works quite well.
The main purpose of these old analog controllers is for X68000 use, but there's a hand-full of PCE/MD/MCD/32X and even a few FM Towns and PC-98 games which support it as well.
Here's my old PCE Analog demo vid.