Mednafen is the only PCE emulator worth using and it's still not perfect. For one, it has no GUI and the only real frontend kinda bites.

I wound up just writing a small batch file for whenever I wanted to play a PCE CD game (I don't bother with the HuCards...nothing there interests me) and it works dandy (with the exception of the hidden bonus game in Dracula X not working last time I checked and a single sprite priority problem in both Exile and Ys).