There are also various spa specif products for this- I've used Baqua and Brilliance's (same stuff, or at least it used to be) surface cleaner with good results. It's a gel that you apply with a scrungy pad thing, and it can be used with the water still in the spa or when you drain it out. Gets off all kinds of stubborn stuff, like the notorious Baqua Scrunge, etc.....
It's very effective at removing waterline deposits too.