It is definitely all personal preference but i'll give my $0.02 cents opinion
All Sega i personally use Hexaeco for everything. The Hexaeco core may not be as up to date as the standalone GenPlusGX but it is still great. I love RA-Hex frontend and bezel support is icing.
TurboGrafx is best played with standalone RA 1.19.0 i released. CHD is supported and Turbo toggle works beautiful plus all other standard features are present. It is missing bezel support though. Hexaeco is a good option since everything is very good/great but CHD is not supported. WiiMednafen is also outstanding but again CHD is not supported.
For NES i use TX, it simply is better than everything else. Next would be GX, then RX. Hexaeco offers bezel support so definitely worth mentioning
For SNES, take your pick of GX, RX, TX. I personally use TX here also but all 3 are great SNES emulators. Hexaeco is your alternative here again with bezel support and the SNES Next has very good speed and compatibility. Stay away from vanilla RA SNES.
Sega 32X first choice is RA recompile by
@SaulFabre that i recently got working as standalone. Hexaeco has minor issues but does have a workaround for full speed.
Neo Geo is solid with both RA recompile standalone or Hexaeco standalone. RA has a little better compatibility but Hexaeco (again) offers bezel support.
Neo CD. Niuus RX release is damn solid but the recompile standalone is superior in every way.
GBA... mGBA standalone is above all without question. RA mGBA standalone is pretty outstanding plus offers full screen support for gb/gbc if that makes a difference to end users (i does for me)
emGBA is also very very good and really your only other standalone option if you pass on the others mentioned.
Just my opinion. Feel free to join the conversation and voice your opinion guys...