I think it's not fair to choose one emulator among the wide variety of systems.
You have also to take into account that it's not the same programming a GBC emu than GC or PS2 emu. For this we should also consider the optimization of the code (a bad optimized GBC emu could run in nowadays systems, but would not be as "good" as a good optimized one).
We should think as well of the most innovative feature included in an emulator. GB linking, hardware rendering (soft rendering in the case of N64, which would allow more accurate graphics in detriment of quality), etc.
For this latest point I would choose Rice's plugin, with which you are able to replace original low-res textures with hi-res ones. Simply amazing, just take a look at Federelli's, Djipi, Mdtauk and Macphisto threads!
But I remark it's not fair choosing "the best emulator ever". It just makes no sense...