The NSA pitching rules are pretty much exactly the same as ASA. They do not allow the backward step that is allowed in NFHS/high school.
I can't think of too many others off-hand, besides the EP/substitution/courtesy runner already mentioned.
One oddball rule that I can remember coming up once in twenty years is that NSA prohibits the batter, when she becomes a batter-runner, from carrying the bat with her all the way to first base. This is an out in NSA, not in ASA or NFHS.
With all the changes ASA made this year to their double first base usage, I can imagine that there might be some differences between the way NSA interprets some plays using the safety base.
If I recall, there are some minor differences to the NSA approved bat list as compared to ASA and NFHS.
I have run into some issues with NSA umpires that seem to be well versed in SLOW PITCH rules, but tried to apply these rules in a FASTPITCH game with miserable results. For instance, in NSA if a slow pitch batter hits a foul with two strikes it counts as a strike and the batter is out. If the third strike foul is a caught fly ball, the ball becomes dead and runners may not advance. Actually had an umpire try to enforce this in a fastpitch game one time!
I have had one NSA umpire tell me that it is an NSA interpretation that a batter running on an uncaught third strike, when she is not allowed to, is to be considered interference. Yet, I have had another tell me that this is not interference and is ruled the same as ASA!
One good thing about NSA: they publish their rule book on-line. For 2006, they have also put together their first case book and it's on-line, too. I see that Bill already found that, so here's a link for anyone else interested.
http://www.playnsa.com/modules.php?name=Content&pa=showpage&pid=7