SHORT ANSWER: Add HDMI and Component cables
Which wires to run certainly depends on how you'll wire each device you mentioned...BUT, in a perfect world, here's what I'd do:
1) Keep the "Cable tv cable", aka coaxial cable. Make sure it says "RG 6" on the cable, not the old "RG 5".
2) Keep the Cat 5e cable (Cat 5e or Cat6) are fine.
Don't use a yellow-colored Cat 5e cable, long story.
3) I assume all the other devices in your media center - your Xbox360, DVD, etc. - will all connect into a true home theater receiver, before that Receiver will in turn pass that signal along to your TV. If that's true, and the receiver is new (<1yr old), then all you should need is a single HDMI cable to pass all those signals along. HDMI does both the audio and video for digital sources.
An older reciever may not upconvert those other video signals through HDMI, though, so you'd need to run a component (Red-Blue-Green) cable as well to cover maybe the Wii, a VCR, camcorder inputs, etc...AND a matching pair of RCA (white-red) for the audio there.
If you're NOT using a reciever, i'd say it's a good time to get one...otherwire you're going to running a hell of a lot more cables:
Xbox 360 - hdmi
Blu-ray/PS3 - hdmi
Wii - Component
Cable Box (if any) - hdmi, hopefully
DVD player - component + rca
VCR - rca (yellow) or s-video + rca (red-white)
Camcorder, etc... ????
See what i'm saying?
Good luck - hit me back if there's something else.
