You may look into WinLIRC (http://winlirc.sourceforge.net/), the Windows port of the linux open-source LIRC package. With an IR xmitter(s) and receiver connected to your serial ports, you can use ANY remote (or even an IR keyboard) to send commands to LIRC, which will then perform your PC commands or send learned IR signals to your other equipment.

You can get equipment that is perfect for the job cheaply here:
http://www.irblaster.info/
[Link: irblaster.info]

good luck!

j