yes, i have noticed a big delay, ~10 seconds, in sound playback on stella (Atari 2600 emulator) as well.
it must be an issue of stella or in combination with raspbian or so.
to be sure, i just (2013-09-20) installed stella on a brand new virgin raspbian image (+update, +upgrade, +rpi-update), and i got still the same issue.
aaarrrr... crap - i am pretty sure, several month ago, i was using stella without that issue on my RPi - but i can not remember what version of stella and raspbian i was using - and now, after many many updates ago in the past, i don't have that image anymore.
EDIT: "export SDL_AUDIODRIVER=alsa" does not fix that issue.