I have a system with many similarities to Wuench, except that I used HomeSeer instead of CQC as the "higher logic brain". But I'll concentrate most of this discussion on what I consider the more important aspects of my system...
My Elk (for security and some inputs) has been extremely reliable but I echo the fact that they have been stuck in time in terms of updates to their interface and some technology (for reasons I just don't understand), and require a Windows -based software to program the system. They deserve consideration as a security system that can interface with HA, but their lack of innovation worries me to the point I would also look at HAI if I were building new, and decide between the two. I can't make a recommendation beyond that except to say that security MUST be rock solid and I strongly advise it be capable of operating on its own if other components "go down".
Lighting for me is Insteon and an ISY. I despised Insteon for about two years in a previous house but they largely cleaned up their act and dramatically improved their quality to the point I installed them in our current house and have been generally pleased. I went with them because it was an existing house so a rewire was not practical. Zwave was my other consideration but I was concerned about the controller problems others seemed to be having with it at the time, and the mesh network just wasn't what I personally wanted. I have nothing against it, though, and others will be a better guide re that. For NEW construction you can't beat a hardwired system for reliability, but you must get things right the first time and plan ahead for almost anything you want for the future (wires being the limiting factor). The prior owner of our previous house had installed some hard-wired system that I can't even remember now, and by the time we bought it ~3 years later it was essentially impossible to upgrade so that it could work with a HA system. We ripped out thousands of $ worth of new-looking but obsolete hardware and put in Insteon. If I had to do it all again Insteon would be on my list along with Zwave largely because I I could reconfigure and add as our needs change over the years (and they do, more than you think, unless you automate everything possible the first time). And even then it's a gamble.
For lighting control I also use an ISY and it has become my favorite part of the system. Almost as reliable as the Elk, and the best customer support imaginable. And they continue to innovate, with great response to the needs of their community. I tie it into the Elk with their Elk module (via IP), and it's as if it were a single, integrated system. In fact, I'm in the process of upgrading to a new ISY 994 that adds Zigbee support for energy monitoring (not for lighting control, although that could be a fallback for the future). Their only downside is that the user interface for programming is very klunky and they have no plans to invest heavily in UI themselves, preferring to let 3rd party apps handle that. Frankly that may prove to be the best solution, but I continue to look for a great User Interface as WAF and my own desire fir things that "just work" and have good design make this more and more important. At any rate, ISY (company is actually Universal Decices) recently added support for Zwave and Zigbee, and they make a great product with amazing support. I strongly endorse them.
For HVAC I took a near - heretical approach for hard core HA enthusiasts and went with a Nest after years of using a serial-based thermostat tied into the Elk (and an even older X10 tstat before that). Love the Nest! Rock solid performance, great user interface both physically and over internet, and great WAF. They do not have an open API but some programmers have figured out how to interface with it for third party plugins to the software "brains" of a HA system. And frankly, I don't know that I really need much more control than that provided by the Nest on its own. It can be accessed physically and even a child can easily understand how to operate it. The web and app interfaces operate beautifully and easily, programming is done through any of these methods and it does a better job of interfacing with our 10 year old equipment than any other HA stat I can buy. I can see exactly when the system was operating each day (including when backup heat for the heat pump was required) and they even email me each month with an easy to read summary. It vies for "favorite component" with the ISY and I strongly recommend it.
For higher logic brains (the equivalent to CQC for Wuench's system) I think it's important to NOT have critical functions DEPENDENT on this part of the system. I liken it to the human body in that we have a part of our brain that controls speech, reasoning, etc., and we're happy that we have this. But if we suffer a blow to the head or even when we go to sleep, our brain stem and "lower order / less evolved" brain functions continue to operate (heartbeat, respiration, etc.). THAT is how I recommend you build your system. If the higher logic brain goes down, you want HVAC, security and maybe even basic lighting control to continue to function adequately.
Now, I admit that I am looking for a new "higher logic" HA brain. I used HomeSeer for years and was happy with their version 1.x (many updates). Then they came out with version 2.x and personally I have never liked it due to continued problems with reliability (others, and your, results may be different so let them chime in). They now have version 3 released and in beta and the jury is still out, in my opinion. It's a Windows-based system and we are increasingly a Mac household, and when I hear them talk about things like "memory leaks" they are finding and attempting to fix I start to become concerned. I have felt like a beta tester for them for years and have grown weary of it, although I have not completely walked away. The HS community of users is fantastic and frankly much more helpful to me than the company, whose support I find spotty and focused on their latest product and interests. I have it shut down now and am seeing what I can do with the Elk, ISY and Nest only. WAF has improved dramatically, and I miss only a few functions such as some temp reporting and speech warnings of weather alerts, visitors, etc. I suspect my search will continue for a few months to come and include both the new HS3 and others. Most of my energy will be going into the new ISY, though.
I hope this summary and opinion is of some value, and welcome to the addiction.