Since you are building Home Theater PC box, not ordinary desktop, you don't have place for standard keyboard and mouse. Instead, you will need decent remote controller, preferably one with RF or bluetooth link (stay away of those cheap IR remotes, because they require optical line of sight between remote and IR receiver - bad reception aside, you don't want bulky receiver dongle hanging around your TV set). Both RF and bluetooth have their advantages being RF more simpler (does not require device pairing) and bluetooth more standardized so you can use one receiver (USB dongle attached at the back of your box) for multiple devices: remote controller, keyboard, mouse, headphones and even your cell phone. If you choose bluetooth, be careful to pick one that allows simultaneous connections to more than one device (the more, the better).
For initial setup and later emergency interventions, you will need some kind of keyboard and mouse. Because in front of your TV there is no suitable surface for classic mouse, you will want keyboard with integrated mouse controls (like small joysticks). Although you may not plan to use your keyboard/mouse very often, I strongly suggest that you go for wireless option (another possibility if abusing your front USB ports when you need classic keyboard/mouse).
My choice for peripherals was ATI Remote Wonder remote controller and BTC 9019URFIII Wireless Multimedia Keyboard. Remote Wonder has some issues with detecting key presses (often it detects too much of them) and I needed to patch kernel driver to get all the keys working with my X.Org/Openbox combination. It is of first Remote Wonder series which you can't even buy anymore, and I don't know if Remote Wonder II is any better. Try it before you buy it, because remote is the most crucial HTPC peripheral. With BTC keyboard on the other hand, I had only pleasant experiences.
