Up until last year, I would have to guess that overall, not that many natural 20's when playing a d20-based game, and a grand sum of three from playing 4e.
Reason I say "until last year" was that was when I started playing Zayne Morningfire, a young Jedi in the Star Wars Legacy Era. While he doesn't score that many nat 20's on his attack rolls or other skill/ability score checks, the boy seems to roll nothing but 20's on his Use the Force checks, with one session rolling 15 nat 20's out of a total 17 Use the Force checks, which is probably more natural 20's than I've rolled for any other character in a d20-based game than I've ever played, and that was just one sessions.