I'm going through the same process w/ my home remodel. I want to run some components in the garage and the display in the media room. I'm going to assume you already have a method to run the video/audio line to the TV, which alone has it's own can of worms.
For the remote, the RF remote suggestions above are very doable. Another choice is to use an RF remote converter.http://www.weaknees.com/rf-remote-details.php
It's relatively cheap and it works w/ many remotes since the RF portion is actually built into the battery. I've used it very successfully with an URC6131 remote. I use those because of the DVR buttons and it's CHEAP, <$20, looks like it even has a new version, the 6131N. You can drop/break 'em and replace 'em. I've had them work over 50' through walls w/ no issues. Sadly, I couldn't get it to work with my Harmony 688 or 659. I think the cheaper remotes emit more RF during the button presses, which this unit relies on.