Well, like I said, the software I'm most familiar with is the Linux Infrared Remote Control (LIRC) project. The heart of that project is a server that sits and monitors the infrared port; it also includes a suite of command-line tools to support receiving or sending commands via the server.

There are also a wide variety of LIRC front-ends, tools, and ports to every operating system imaginable. (And yeah, you can find LIRC on the N900 and on Android, though I don't think there are currently any cell-phone-sized devices with CIR receivers.)

I can't really give you a one-size-fits-all approach to choosing and setting up an LIRC package, as it really depends on you as to what you want to use it on and how you want to use it. But here's a link to some of the LIRC software available:

http://www.lirc.org/software.html