Hello Paul,
The general rule of thumb is to cable as much as possible during your refurb as it's much cheaper and easier to throw in bundles of cables at that stage than when everything is complete and somebody decides that the TV doesn't "work" in that corner of the room and needs to be moved elswhere!
The wiring guide on the AH site is a good place to start (
http://www.automatedhome.co.uk/conte...ing-guide.html).
For your media distribution, few on the forums will argue against using Plex - there's servers available for most NAS devices, or it will run on MAC and Windows. And there's clients available for just about everything - I use it on iOS, Android and on Samsung TVs and BluRay players. I've played with Western Digital WDTV devices (with alternate firmware which are *really* cool) and the RaspBMC build of XBMC for the Raspberry PI - these are great, I used to have one of each in every room :-) But I moved to Plex as it pretty much "just works" out of the box, indexes all my media really well automagically and with the clients built in to TVs and BluRay players I no longer need any additional boxes at the TV end.
With regards to the Home Automation aspects, it really does depend on what your budget is! Since you're going to be cabling anyway, you could go for a CBUS wired install (although they do wireless too). Or a hybrid system based on Insteon.
My own chosen path at the moment is with Z-Wave - I'm slowly migrating a mish-mash of HA kit built up over the past 14 years or so to equivalent Z-Wave devices. As it's wireless it's pretty easy to retro-fit. So far this has been working very well for me, there's an abundance of devices to choose from, a good range of central "controllers" and the whole lot can be controlled over web interface or dedicated smart-phone and tablet apps.
For heating I'm currently using ELV / FS20 based thermostats, radiator valve actuators and boiler interlock. It works well but has it's limitations and is also has a "hybrid" control system (FHEM and xAP FHEM), so I'm looking to upgrade that probably this year to a Z-Wave based alternative to bring it all under one control system (in my case a MiCasaVerde Vera).
Hope that helps!