I had the house run with a star config, multiple drops in each room, and multiple runs for both rg6 and cat6 to the utilities all back to my central server area. I have a DWR-24-17PD http://www.middleatlantic.com/enclosure/wall/dwr.htm mounted to the studs. Plenty of room in the rack, it swings out and I'm able to access the back. I've been running this config since 2006. I had custom enclosures made for my machines, as the rack can realistically only hold things about 13" deep, but the folks at www.protocase.com made the process of getting custom cases easy.
Here are somethings you really should think about:
Add more drops then you think you will need before the drywall goes up, trust me a few years down the road you will wish you had more.
If you ever plan on getting satellite remember that you need far more runs of rg6 then you would think.
Also think about multiplexing OTA from the attic and the output from a media server from your rack.
Have your builder install a HVAC supply and return in the room that will house the rack.
Most importantly install sound proofing in all the walls around the rack, consider even adding a muffle on the bottom of the door.
Plan to replace fans with quieter ones, and harddrives with quite or silent ones.
Get a good UPS for the server room.
Get a good firewall to cover the entire house and allows you to place a machine or two in the DMZ.
Use separation on the switch to keep the wifi/LAN/DMZ separate
Have all the cables simply terminate at a patch panel, trust me this will save you a headache when you need to reorganize something. Also do not let the builder install any of their usual splitters, say for phone distribution, as they tend to degrade the signals and if you run it to the patch panel you can map the rg6 and cat6 drops as needed, and split things with higher end equipment. The builder will likely add a surcharge for everything they do. So stick to just have them run the cables, sound proofing BEFORE the drywall goes up, and framing it proper for the rack if you want to attach it to the wall.
My builder used a structured wire panel insert in the wall which makes sound proofing that portion nearly impossible.
I found that my builder was unfamiliar with networking and I had to redo several of the drops that did not test right. So you might be better off not having them connect it up and getting your own patch panel that handles multiple types of cables.