In celebration of the NBA 2K12 cover announcement, IGN took a look back at MJ's appearance in video games over the years:
http://xbox360.ign.com/articles/118/1185125p1.html
NBA Live 2000 stands out as a sentimental favourite for me, NBA 2K11 would top the list in terms of quality (though I still say 2000 was a great game for its time and certainly a high point in the NBA Live series). I've still got Michael Jordan in Flight somewhere too.