I use iTunes for everything that I put on my iPod (which is pretty much 99.9999999999% of what I listen to) so the play counts are consistent. If I need to play a song for some other reason, like if I need to listen just to the end of a song so I don't want it to +1 the song's play count, then I use Winamp. I also use Winamp for the .0000000001% of songs that I don't have in iTunes and don't want to put there, like all the crappy quality rips of new Ayu songs when they leak.
I can't stand WMP and playing audio files with VLC just feels so... weird and wrong.