I have been running a MacBook Pro like this for over a year, with no problems.
However, as Beoberlin points out, you do reduce the cooling some, which means that the fan will kick in - and that can be noisy.
I wake up the Mac using the Apple remote or my mobile phone (which has Salling Clicker installed). It also works with keyboards/standalone mice. There's a keyboard from Logitech that has an integrated mouse/pad, and that also looks quite nifty.
There's also a bit of software called Buddy Remote that gives you access to all of your programs through the Apple Remote, which I'm going to try in this mode.
A friend took away the raised rubber pads on his MacBook Pro and placed the computer on a slab of metal, which he claims sucks heat away from the computer. Haven't tried that ... There are settings you can use to suppress when the fan hits in, as well as software that will help you do that. I have found that it helps to turn off all apps you're not using, reducing the number of windows, deactivating Dashboard (a real CPU hog) and avoid using Firefox while watching movies/listening to music. Then the fan kicks in very rarely.