In general, I like to use a universal IR remote for the same tasks as I would with a stand-alone DVR, in other words, power, source selection, volume, channels, simple cursor navigation and transport controls (play, rec, skip, etc.). Beyond that, it's much easier to use a wireless keyboard/mouse or smartphone/tablet remote app IMO. Although some MCE remotes have basic mouse functionality, I find it very slow and awkward to use in practice. It's fine in a pinch and works fine on any universal, including harmony, but if that was my only navigation tool, I'd go insane.
Although harmony is easy to set up and is very popular, nearly any universal remote can handle MCE tasks just as well. I personally find harmony's capabilities extremely limited and their failure rate after a few years of heavy use to be high. So I use other remote brands.