On mac os x (10.5.5 intel), Processing 1.0 (0162), when exiting a sketch (both in present mode and normally) if I use file->quit or 'command' 'q' instead of
esc, the stop() method isn't called.

I'm assuming this isn't intended behavior, sorry for wasting someone's time if it is!

This can be easily reproduced like so ...

void setup() {
size(100, 100);
}

void draw() {

}

void stop() {
println("test!");
super.stop();
}

now try exiting the sketch with esc, with file->quit and 'command' 'q'

Hm, this is really difficult to fix because it requires a bunch of
Mac-specific handling code since the Quit menu is handled very differently
on OS X. But I'll make a note of the problem, perhaps someone can pitch in
and give us a hand with it.

Well it's not a big inconvenience as far as bugs go, thanks for taking a minute to check it out.
Hopefully someone will have time to whip up a fix eventually.