I have used Helicon, CombineZF and Photoshop. For straight on pics, where the subject's plane of focus is not at an oblique to the lens, in my application...the dial of a watch straight on...with the image stacks dial, applique indicators, hands, tip of hand pivot, bezel, then I find CS4 does a good job.
Where the subject is at an angle...say the dial is flat on the table top, and lens about 45deg to the dial, if I want to stack images from front...ie bottom of dial at 6...to the back...top of the dial at 12, then CombineZF is better.
I find Helicon is roughly similar...having tried only the free trial version, so elected to stay with the free CombineZF. But a good friend who also shoots watches in Germany uses Helicon in his studio with good results.
I feel the steps to move the focus position more critical...I use a Manfrotto macro focussing rail, moving about half a turn of the screw. For my application, this is adequate...my aforementioned friend mounts his camera on an old Sinar P which he bought when he was a student.
But I think the more elegant solution is to use a special, computer driven rail made by these fellows -
http://www.cognisys-inc.com/stackshot/stackshot.php- surprisingly, they are actually cheaper than the manual RRS macro rail.