The system's are the same I think, you can just change the language I bet and you can't tell the difference between Japanese and American. The only differences will be PS1 and PS2 and DVD playback because they are region protected. PS3 and Bluray will be the same in either. I might be wrong. Anyone disagree?
European will not play on either JAP or USA systems.
PS3 games from any region can be played on it. As far as online, some games run on dedicated servers (Resistance), meaning only being able to play people from Japan online.
PS1 and PS2 games are still region locked, so no US or Euro games.
Only region 2 DVDs can be played.
As far as homebrew programs, loaders etc.. your guess is as good as anyones. But I'm sure they would run on all systems, firmware version being the more important thing to look for.