So the four products we're going to consider here are:

• Zerene stacker
• Tufuse + Tufuse Pro
• CombineZP
• Helicon Focus

Zerene stacker

Advantages

• Ease of use
• Good retouching features
• Quality of output
• Available for Mac and Linux as well as Windows
• Stereo output available from single Z-stack

Disadvantages

• If you want to sell your stacked images then it's one of the more expensive packages, however if you are only interested in personal use then that license is pretty cheap considering the overall quality of the output.

Tufuse + Tufuse pro

Advantages

• Relatively easy of use
• Output quality is good
• Reasonably cheap

Disadvantages

• No alignment functionality
• No built in retouching facilities

Combine ZP

Advantages

• Completely free
• Output quality is good
• Reasonably easy to use

Disadvantages

• Quality of output definitely not quite as good as Zerene
• Interface a bit quirky
• No built in retouching facilities

Helicon focus

Advantages

• Very polished interface
• Has some funky extra features like 3d surface map generation
• Easy to use
• Fast

Disadvantages

• One of the more expensive stacking packages, especially if you want the Pro version for the built in retouching functions.
• Personally I was never totally happy with the output from Helicon, although I have to confess I've only played with the trial version for a couple of weeks. I know some people can get good output from it so the best thing to do would be try the trial version and see what you think!

I have the paid shareware version of Tufuse pro, the freeware CombineZP and the paid professional version of Zerene. However I have only trialled Helicon for a month, and that was a long time ago.

To be honest the only reason I can think not to recommend you immediately buy Zerene stacker is if you definitely want to sell your focus stacked images and you can't afford the professional license. The output is best in class. The user interface is good, not quite perfect yet but close. The retouching facilities are the best I've come across.

Having said that, I would definitely recommend you download and try CombineZP as it is totally free. It's output is very good and there's probably no reason why you need more than this software offers.

Considering there are free trials of both Helicon and Tufuse pro, I would also suggest you download these and give them a go, your tastes in software may well be different to mine.

Full disclosure note - Zerene stacker is written by Rik Littlefield, who is the editor/administrator of Photomacrography.net, where I am also an administrator. I consider Rik a friend. This does not mean I have recommended Zerene because Rik is my friend, or because I would get any benefit from you purchasing it. I just honestly consider it the best software available currently for this task.