Lighting:
If you go with z-wave, you would need the VRC0Pv3 (or +3) to control the network with Premise (once the network is setup). It's an RS232 controller that bridges the z-wave network with an easy to use ascii based protocol. I also use the Leviton USB stick and the RF Installer Tool you can download from Leviton's site for free. The USB stick is only used to setup the z-wave network. After that, all control is done via the RS232 VRC0P.
I use a 50 node z-wave network with Premise: thermostats, lighting, high power relay and some kwikset locks. Most of the time the lighting is very responsive, but one or two times a week it takes a few seconds for a light to come on. The issue isn't with Premise, but didn't appear until 6 months after I setup the network. Z-Wave is a great retrofit option aside from that. I never touch a light switch, so lights are usually toggled via z-wave and hardly ever local manipulation. I've seen a very low failure rate with z-wave commands, just a slight delay every now and then.
The other issue with z-wave is that you can't quickly (less than 500ms) turn off 40 lights at once unless you use scenes (e.g. don't plan on sending 40 on or off commands at once). The drawback with scenes (at least on the Vizia RF dimmers) is that it takes several seconds for the status of each light to be received by the VRC0P. I haven't tried the Cooper AspireRF lights, they may not do this. I primarily use the Leviton ViziaRF+ line.
To make the z-wave issue even more complicated, all z-wave dimmers that I have used rely on the load to provide neutral (through the lamp's filament). As you might guess, this causes havoc if the lamp burns out as this removes control power from the dimmer. You will see many z-wave transmission failures as a result (since each dimmer acts as a router in the mesh network). However, after a bit the z-wave network is supposed to be self healing, so the commands eventually go through to the other nodes, but with noticeable delay until you change the light bulb.
Definitely, to avoid this, find a dimmer that requires neutral be present in the box (to complete the control's power circuit). The 15A switches VRS15 by Leviton do this, but they are not dimmers. This also means that your electrician should ensure neutral is present is all junction boxes. I'd also request they use the deep plastic boxes, although the z-wave antenna is toward the front on most switches/dimmers.
I'm not sure what wired options there are for DIY lighting besides UPB. I would assume the professional solutions require you to run all power cables for lighting to a common location, so this is something to think about in advance. Home running every lighting circuit would be expensive as would whatever proprietary controller one would use, but this would be the most reliable. You could use din mounted relays and make your own lighting controller, but I'm not sure what the housing inspector would say about it.
A third lighting option that is supposed to be good is RadioRa2 line by Lutron. However, I'm not sure what RS232 controller you would use with Premise. I know Premise natively supported the RadioRa line.
Security:
I've read a lot of posts with folks having trouble with wireless alarm sensors, so I definitely wouldn't use them unless it was necessary. The HSM z-wave motion detectors can also respond slowly, so I wouldn't use z-wave for security sensors.
My favorite motion detectors are the ceiling mounted round ones as they look very nice: http://www.dsc.com/index.php?n=products&o=view&id=1303 I think there's also a dual technology version too.
I chose Elk for the alarm system. It seems you have two choices Elk or HAI. The native Premise HAI OmniPro add-in is closed source. The Elk M1G Premise module is open source, so you can always modify it as needed. I modified it to use the new Elk two-way wireless keyfobs, but I need to post the updated version. If you use HAI for lighting (I think they offer zigbee and UPB), you might want to make sure Premise supports HAI lighting or make your own updated OmniPro II module for Premise (using the Elk module as a template).
The M1G is responsible for controlling occupancy in Premise. Premise then triggers the lights as needed to the appropriate level based on time of day. I don't use the M1G to directly control my lighting, but it's possible. I'd rather keep all the logic in one place (Premise server). This has advantages as you can send text updates to the M1G keypads (weather, etc...) using Premise. You can also use the keypad function buttons to trigger things in Premise. If you buy the new Elk two-way keyfobs, you can use them to trigger things in Premise in a similar manner. There's also output relays you can use with the M1G allowing Premise to open your garage door, turn on a fire place (assuming it uses a low voltage control circuit) etc... Basically, the ascii protocol that the M1G uses will allow for seamless integration with Premise. I'm sure the same can be said about HAI, but I haven't used any of their products so I don't know the level of integration that's possible.
OBi110 with Premise:
123 and I developed the module. I use Premise to pop-up a message of who's calling in Media Center (using the vmccontroller MC add-in). Dialed call logging doesn't work with google voice, but will work for voip or land line. Incoming calls
EDIT: Other stuff to think about...
I would consider running conduits when possible. Perhaps all your conduits could run straight into the attic giving more flexibility later on. Then you would have several large conduits to get from the attic to the basement via a chase (or where ever you end up terminating everything).
Use the largest structured wiring boxes possible.
Network based IR control to turn TVs off when you arm away etc... I use a Global Cache WIFI2IR and GC100 controllers.
Distributed A/V would be neat, but may not be needed if you are using XBMC.
