Overclocking for reduced slowdown:

Mesen: Options -> Emulation -> Overclocking -> Additional scanlines before NMI: 240
puNES: Tools -> PPU Hacks -> Enable Extra Scanlines -> Postrender Lines: 240

Use "VBlank (scan)lines" or "after NMI" instead in rare instances where games might be broken. 
Do not change the clock rate in Mesen.
