There are a number of options on I/O hardware. For those devices close to the controller, just put in a PCI-based multi-port card. It's inexpensive and the most robust way to do it. You can run cat-5 serial cables a pretty good ways without problems.
When you need to go beyond that length, then you can get ethernet-to-whatever converters of various types, but they tend to be a bit pricey because there's just not enough of a market for them to drive the price down. USB based ones are cheaper, but you can generally just run a cat5 serial cable further than you can run a USB cable.
The Global Cache's serial ports are fairly useless because they are so limited in terms of settings. They do n-8-1 and that's it, with a fairly limited range of baud rates. That really bugs me about the GC-100 since if they would take care of this issue, they'd have a killer device. It's already a nice device and our customers use them (and I use one) but just for the IR/contact closures, not the serial ports. Plenty of devices use odd or even parity or require the use of some of the control lines or have faster baud rates than the GC-100 ports can handle .
These folks have both multi-port cards, and IP and USB based multi-port boxes:
http://www.comtrol.com/
http://www.quatech.com/
These folks have good USB based multi-port boxes. I used one of theirs in my home theater:
http://www.ionetworks.com/
In most modestly sized homes, you could probably do a 'home run' type of scenario with multiple cat-5 serial runs from each room to the central closet to be used for various things, serial control among them, and just use on-board PCI-based serial ports in the controller (placed near the central cable panel) for serial devices. At least that's one option to look at.
CQC is network distributed, so you can certainly distribute control around if you want. You can have a separate machine in the home theater for that control if you want, and have a separate one in the central location for overall home control. If you choose to use CQC in this way, they will be completely aware of each other and you can control anything from either of them, have some devices being tied into one machine and some into others and so forth. And you can install the client services on your daily use machines for just client side access to the system (i.e. not actually controlling anything, just provding graphical interface access to the automation system, so there is no danger to the HA system going down if these systems stop working or are turned off.)
If you want a wall mounted touch screen computer, there are products like this:
http://www.nobu-usa.com/Product/12TouchPanel.htm
And it can be the overall home controller as well if you want, via external ports.
Or (less expensively) you can just mount a standard touch screen on the wall and use a KVM extender to run the touch-screen/video via a single cat5 back to the control computer in the closet.
We are also now testing out the support for devices such as these for portable interfaces for CQC (in addition to the obvious ones like PocketPCs and SmartPhones):
http://www.kubecorp.com/data/Pdf/RV10TS.pdf
http://www.tatungwebpad.com/htm/product_content.htm
Anyway, it's a big subject, and unless you want to pay someone to put it together for you, it can be a big of a job to explore all the issues. There's a lot of info about the subject in general on the CQC web site, so you might want to read through some of that. In the Documentation section.