2. Mesen - This one acts like the real system. I also use this for music hacking as well since cdl doesn't work on NSF files on FCEUX anymore on version 2.2.3. Another nice thing about it is while using the cdl, you can see what the colors is doing in hex viewer in real time. In CHR Viewer, you can pick on a tile and draw like in Nesticle.
Note: The only way that I can tell if the emulator acts like the real system by playing "The Guardian Legend" by typing in this glitch password:
6666 6666 6666 6666
hhhh hhhh hhhh hhhh
And it starts on "Area 2" out of the map. Sometimes "Area 1" and on most emulators, it starts on "Area 0" and sometimes "Area 1". That's the only way that I can tell.