I've been experimenting with this method for the last several weeks, working to understand when it works, how it fails, and so on. Of course there are a bunch of interesting interactions, and I'm really not ready yet to write up what those are. But the bottom line is that the method looks very promising --- I'm excited.
Last night, I finally decided it was time to post out a first look and let you folks know about this new direction. (Or maybe it's an old direction. As the TuFuse page points out, what's being used are in some sense fairly minor enhancements to "a multi-resolution fusion technique first described 25 years ago". I guess sometimes it takes a while for things to click!)
What's shown below are side-by-side comparisons of TuFuse and each of the other four commonly used methods from Helicon Focus (HF) and CombineZM (CZM). Clicking on the "Animated comparison" links will get you animated gifs that alternate each pair of methods, overlaid on exactly the same screen space so that differences jump out at you. I strongly recommend to look at the animations -- you'll be shocked at how much more you see.
Note that TuFuse only works with pre-registered images. This stack was shot with a traditional macro setup, so there are scale differences between frames, and the stack is not suitable for direct input to TuFuse. To generate registered versions of all the frames, I first ran them through PTGui. This process does an extremely good job of registration (far better than either Helicon Focus or CombineZM, for difficult stacks). Unfortunately for this type of stack it also requires guru-level knowledge of control points, lens distortion parameters, etc. etc. I'm chagrined to admit that I messed it up several times myself, and I probably know that area as well as anybody else on the planet.
Not to worry, though. I'm quite confident that it's only a matter of time -- and probably not much -- before some variant of this method gets incorporated into one or more of the standard tools that already understand how to deal with deep fuzzy stacks. That'll be nice!

The images shown here are crops, resized in Photoshop to 40% of the actual pixel size coming from my 300D. No other post-processing except for minor level adjustment, applied uniformly to all images.
All tools were fed the same set of pre-registered images; I just turned off auto-alignment in HF and CZM. Version numbers were Helicon Focus 4.40 Pro; CombineZM February 3, 2008; TuFuse 1.34. Default parameters for all packages except as specified here for TuFuse.
--Rik
PS. Late-breaking news from email a few minutes ago is that there's an even more recent version of TuFuse ("latest beta version of TuFuse Pro (0.9.3)") that includes some other improvements for deep focus stacks. I haven't tried it yet...
Edit: I see I failed to remove the post-sharpening step in the two CZM macros, so those two images have actually been sharpened a bit compared to the TuFuse output. It's a minor difference, but it explains why a few details look more crisp in the CZM images.

Animated comparison.

Animated comparison.

Animated comparison.

Animated comparison.