If you want to use IR use this: http://www.usbuirt.com/ along with this: http://www.girder.nl/.

The USBUIRT is an IR receiver that plugs into your USB port and recieves a variety of different frequencies.  Girder allows you to script actions based on that input.  It's a nice setup.  I use it currently on my SageTV HTPC install at home.  I don't switch audio inputs however but if you can do it with a mouse Girder will allow you to do it via remote.