A couple:
Silence is golden, sounds you wouldn't normally notice become annoying when your trying to hear what is being said on the movie your watching.. Use a quality silent model power supply, don't go overboard with fans, use a fan controller, use a Zalman heatsink. (make sure you get a micro-atx board that the Zalman fits on!)
Lights are distractions, don't cover the case with lights, use lighted fans, cold cathodes, etc.. The less light the better. Choose a case that looks right for it's planned enviroment, if the enviroment is in a wooden entertainment center then choose a case that looks like normal A/V equipment.
Use a hardware encoding tuner card. The Hauppauge PVR series is the most supported by all HTPC applications (be aware that drivers are a bit confusing the way Hauppauge ships them). Software cards work with some, but miss important features, and use up your CPU encoding.
Software: I have built several media center PC's, on some I've used Windows MCE, on some I've used Meedio, SageTV, BeyondTV, MythTV, and some I've just used whatever program came with the card. I've been most pleased with Media Portal
http://mediaportal.sourceforge.net/
, but it requires a DirectX9 capable video card and a fast machine to run best.. Every program offers different features and drawbacks, so look for what suits you.. Be aware: MCE records in MS-DVR files which are a bit more difficult to convert and burn to DVD.. If you can't find a program that suits you, there are front ends that allow you to "build your own" solution such as Xlobby and Centrafuse.
http://www.mp3car.com/vbulletin/forumdisplay.php?f=60
Oh, and get a MCE remote..
http://www.newegg.com/Product/Product.asp?Item=N82E16880100853
It's supported by most every HTPC program, and it makes life simple..