Fortunately nowadays things have changed. Not only can you find a wide range of HTPC chassis to choose from on store shelves, they come from known names in the case business like Antec, CoolerMaster, Lian Li, Thermaltake, and many others. In addition, prices on HTPC chassis sell for the same price, if not lower than many full-size desktop cases. When you combine this with the fact that chipsets have more features integrated into them than ever before, you can build yourself a pretty powerful HTPC for the same price, if not less than a typical gaming rig.You can check it out over here.
How to build a HTPC

FiringSquad has dedicated an article on building a Home Theatre PC: