Haven't been able to find a top 500 for the original AFI poll, but I have found an AFI Top 400. As with the 100, some reasonable choices (some of which, IMHO, should have made it to the 100 list), and then there are some utterly inane choices. What is THE LION KING doing anywhere near a list of the greatest American films of all time? And Richard Fleischer's 20, 000 LEAGUES UNDER THE SEA?!
There were some good films in the Top 400 that should have made the 100, though. They had the raw material for a better Top 100 than they ended up with.
Re: gangster movies, my list is pretty similar to yours, but I would also include most of the 30s Warner gangster movies, such as THE PUBLIC ENEMY, and Raoul Walsh's THE ROARING TWENTIES. The montage sequences in THE ROARING TWENTIES are amazing, and of course there's the ending.
Re: Mad Scientists and Dwarfs, I can't think of many films I've seen, apart from the FRANKENSTEIN series, that have mad scientists and dwarfs in them, let alone mad scientists and dwarfs torturing naked women.
Re:Preminger, THE MAN WITH THE GOLDEN ARM is great, lots of amazing camera movement which must have needed endless preparation to make it seem so effortless, the camera seems to fly. WHERE THE SIDEWALK ENDS is on my must-see list.
As I've typing this, I've been looking down the Top 400, and I have one more thing to say: JERRY MAGUIRE?! I hope they weren't really serious. At least it didn't get onto the 100 list.