The way I see it, if you're going to do this you might as well get as much flexibility/versatility as you can. Those little off-the-shelf media centres are great for folks like my mother, who want things that can just be plugged in and used; for someone like myself (or like you, from what I'm reading), a custom-built rig seems like the better option.
If you're worried about cost, you could always go with MythTV -- it allows you to run the backend server separately from the frontend, so you can stick the backend on your home server which is probably powerful enough to do the heavy lifting and leave the actual HT box to just handle the GUI and streaming. You'll still need something reasonably powerful, though; avoid anything built around an Atom or similar processor and you should be fine. A barebones SFF PC can be had that'll do what you need for $200ish.
On the other hand, spending $400 to $500 will net you a full-featured PC that can handle all of your home entertainment needs. If you build it right, it'll probably even handle some gaming for you, assuming you're into that sort of thing, and it can be made to be silent as well. Building a quiet HTPC is mostly about choosing the right PSU. You can use passive cooling on the processor and graphics card and get the whole thing down to 1-2 fans. At that point you're unlikely to ever hear it, assuming there's any ambient noise at all in your living room. It might end up costing you a little bit more, but setup isn't all that complicated for anyone who is even halfway familiar with computers and it gets you a lot more functionality in the long run.
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I wake up in the morning more tired than before I slept
I get through cryin' and I'm sadder than before I wept
I get through thinkin' now, and the thoughts have left my head
I get through speakin' and I can't remember, not a word that I said
- Ben Harper, Show Me A Little Shame
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