When I'm just casually playing PCE on the PC I use Ootake for the CD-ROM games and Magic Engine for the HuCard games, I know Magic Engine is by far the worst in terms of accuracy, and being paid doesn't help it either, but it feels so good to use! I like emulators that let me do CRT-esque filters, in Magic Engine I can use bilinear filtering + 50% opacity scanlines and it looks pretty good, I'd use it for CD games as well but it can't load disc images, but Ootake is good enough for that, and the CD install option is nice because I don't have to keep mounting the CD image with Daemon Tools every time I wanna play Asuka 120%...
It doesn't have much in terms of filters though, a 4:3 stretch and 50% scanlines are as close as I can get to a CRT look...
I only really use Mednafen to test the Huzak updates elmer sends me... On the PC at least, because WiiMednafen is by far the best emulator on that system, it's exponentially more user-friendly than its PC counterpart, even if playing CDs in it isn't the easiest thing, but it works! Although I mostly just play the Virtual Console releases of CD games if I'm gonna play them, that's much easier, and well, I can get some .wad files with injected CD-ROM images and play CD games that weren't released on the VC such as Asuka 120%, Ys 3 and the Ys 4 fan-translation for example...
One last emulator I also use is NitroGrafx for the DS, but that one is only for when I'm out and about and really desperate to play some PCE (which happens more often than I like), it works with both HuCard and CD games, but the DS's resolution is lower than the PCE so some detail is lost, and if I'm not mistaken, it's using the GB/GBC's DAC emulation built into the DS to do make-shift PCE sound, it works, but the waveforms have their vertical resolution halved (read: there's a loss in sound quality), the volume control is lowered from 32 levels to only 4 levels, so any semblance of attack or decay in the soundtracks are lost, it can't play frequencies as high as the PCE, so a lot of the higher-pitched notes are lost, and it doesn't play any samples, so the drums and voices in a whole bunch of games are missing... Oh and, the CD audio is too quiet...
It's still worth it if you only have a DS or 3DS (like me) with a DS flash cart and REALLY wanna play some Street Fighter 2' Champion Edition or Detana! Twinbee on-the-go, but if you have any other means to play PCE on the go (unless it's PCEadvance) you're better off not bothering with this one...
I'll just patiently wait until someone decides to make a PCE emulator for the 3DS, hopefully 3DSMednafen...