There is another nice piece of software (not free) that is very useful for analysis of IR signals. It also interfaces with various open-source hardware designs for capturing IR signals. The software is called AnalysIR.

NOTE: I'm not connected with AnalysIR, just a really satisfied customer.

I've used the software + a LearnIR dongle to capture & decode signals (including cleaning up the carrier frequency), which I then sent to Logitech for programming my Harmony remotes.

The software also has great code-generation for various controllers, and the stuff I've learned from his blog...