Interesting thread.
Hope you don't mind if I "plug" my own software here ...
USB-UIRT / MCE IR Remote Control - Home
Allows any PC to control devices through IR. Requires a hardware dongle such as the USB-UIRT.
Currently, I'm using my iPod Touch to control my devices via the home WIFI.
The only downside is that you need to have a networked PC running the server software and with the IR dongle attached.
More information on my website:
USB-UIRT / MCE IR Remote Control - Home