Not having used it yet but doesn't SETSPEED configure acceleration for you? By experimenting, you should be able to arrive at a reliable acceleration for your setup.
I don't have a problem with acceleration -- it deceleration. Specifically when interrupting a jog.
I've done some initial experimenting with Dan's suggestion and so far it seems promising. In the custom function where I normally STEPSTOP the motor when jogging I now check to see if my speed exceeds some threshold. If so I proceed to issue STEPSPEED's that cut the speed down by 10% every 20ms until I'm below the threshold at which point I issue a STEPSTOP.
Initial tests have been encouraging. At speeds above some configurable threshold I can come smoothly to a stop with a little overtravel. Below the threshold I am still able to stop on a dime by issuing an immediate STEPSTOP.