I agree that it is by far the worst booking engine of any airline I've used - often it just hangs and you don't know whether to wait or go back or refresh etc.
Last time I booked with them I didn't even get a confirmation email with my booking reference, even though the booking had gone through and my credit card charged - I had to spend 15 mins holding on Jetstar's call centre just to get it sent to me as it should have been in the first place. The other thing I hate are those annoying cross-selling addons like Travel Insurance and Carbon offsetting, some of which are ticked on as default which is very sneaky and underhanded.
Other than that though, I don't mind JQ at all and I've flown with them quite a bit now. None of the DJ "i'm trying to be fun" annoyances and dirty planes, none of the QF sullenness and bitchiness and tired old 763s and none of Tiger's general crapness.