I really miss my Pioneer CU-AV200 learning remote. Never had something like that since. Other than my VCR at the time, all other equipment was Pioneer, so that remote could already control most functions as-is. Just had to have it learn the key VCR functions and then set up some nice "macros" where a single button press could play back multiple commands.
Currently, I just use whatever remote comes with my receiver (currently a Pioneer SC-91). It's frustrating though regarding switching of inputs as there are only some dedicated buttons for directly switching to inputs. And, due to other limitations on input configuration, this leads to having a single "HDMI" button needed to cycle through three different inputs. With a delay of about 3 to 5 seconds to change to the next input (receiver finally displays what source you're on to the TV), this can be a bit frustrating.
As of now, most likely going to move to the Marantz Cinema 40. Really like its remote with dedicated buttons for all seven inputs. So usability will be greatly improved. Though once I move to my next receiver (definitely not Pioneer), I'll now have five remotes to deal with: receiver, cable box, Apple TV, Blu-ray player (most likely Panasonic) and TV (Sony).