Total Control made good points about RS-232: it's fast and usually has a much richer command set, offering more 'discrete' commands.
IR emitters are a nightmare aesthetically, to install, and they definitely are prone to falling off. Cleaning ladies are my enemy when it comes to emitters on cable boxes.
For those reasons, I avoid using them whenever possible. I mostly use Yamaha A/V receivers, and even the $500-retail units have an IR jack on the back that works beautifully. Many AVRs have this support. Sadly, cable boxes have IR jacks, but I've not found any that actually work. Most cheap DVD/BD player lack this also, although Yamaha's BD-A1010 and the Sony ES models have it. You then just need a 2.5mm-2.5mm patch cable from your RF base station to the device: no light, no emitter, and the reliability of an electrical connection.
Impaqt made a very useful note: the Universal Browser in the URC editors allows you to directly enter Pronto commands. I am suspicious of those databases even when they're not learned from a Pronto into my URC remote, since they tend to be 'learned' commands in the first place. The Yamaha PAB website (worth joining for this tool, essential for Yamaha IR/RS-232/IP control doc) has an IR converter that takes Yamaha's published 2- or 4-digit IR codes and converts them into 'Pronto' format - that huge string of endless hex characters. You have to remove the '-' that separate the published IR codes, but it works if you replace them with spaces. Be sure to put the space where the hyphen was, since '7C 8B' generates a different Pronto string than '7 C8B', for whatever reason.
I find that between the 'standard' and 'extended' Yamaha codes, I can do almost anything that can be done with RS-232. Certainly for more than 90% of my installs, and the IR jack on the back makes it just as reliable and almost as fast, and lets me use the much-cheaper MRF-260 or MRF-350 instead of the MSC-400.
For two-way communication, I've never seen enough payback in functionality compared to the effort, especially now that units are FINALLY starting to make good use of their network (Ethernet) ports.
