Among home-theater enthusiasts, Logitech Harmony remotes have always rated fairly high. They're easier to program than most (thanks to browser-based software), they're packed with features (most notably built-in help), and they're quite comfortable to use. However, the higher-end models tend to be pretty pricey: witness the Harmony 880, which originally sold for $249. If you don't mind a refurbished remote, you can pick up a Harmony 880 for just $69.99 shipped.
Although this model is a couple years old, it's still one of the top options in the Harmony line. It features a color screen, charging station, and Windows and Mac compatibility. You can for more details (they gave it four stars out of five--the same as 100 or so Amazon buyers) and/or watch the above video.
I've got the newer Harmony One, which is quite similar except for having a touch screen. To put it simply: best...remote...ever. The 880 still sells new for around $140, so a refurb for half the price is definitely a good deal. The warranty expires at 90 days, but I think that's acceptable given the savings.