There are actually three distinct approaches.
1) Build your own hardware and integrate your own software.
2) Buy a pre-made general purpose PC and integrate your own software.
3) Buy a fully integrated, purpose built, HTPC with all software ready to run (such as an Assassin HTPC).
In my view, it is never worthwhile to follow #2 for an htpc. You'll get an inappropriate piece of hardware in a lousy case that is likely noisy, and you'll still have to do all of your own software integration which is the hard, time consuming part of the process. Indeed, doing the software work will be harder, first because you'll have to deal with all the installed bloatware, and second because the hardware won't be as appropriate for the task at hand as it would have been had you chosen proper components. Plus, if you want an SSD for your OS disk (which you should), you'll have to do even more work.
Putting together the hardware is the easy part. Frankly, with improvements in Windows and drivers and especially the adoption of SATA, it's a lot easier than it was ten years ago. So if you're willing to do your own software integration, you should certainly be willing to pick a case you like and build a proper hardware box.
So the real choice is between doing it all yourself, hardware and software, (#1) or buying a "ready-to-use" true HTPC system with the software already installed like an Assassin HTPC (#3). Just cross off #2.
EDIT - by the way, there was a long thread here recently that perfectly illustrates this reality by a poster who thought he would save money by buying a pre-made box and turn it into an HTPC. Turns out it's noisy, he can't install proper quiet cooling fans in the box, it won't hold the number of hard disks he wanted, and as far as I can tell it's turning out to be totally unsuitable for what he wanted to do. It doesn't save money to buy something that doesn't do what you want or need. He would have saved a lot of time and aggravation, and probably in the end money, and ended up with a lot nicer unit, if he'd just built it from scratch in the first place. As the famous "budget HTPC" thread here has illustrated, you can spend about as much or as little as you want, from $300 to $1000 and up in building an HTPC. You can start with a $29 case or a $1000 case; you can use an i7 or a Celeron. You get to pick something that works for you, but if you do a little homework first, you'll know that when you're done it will work.