Harmony
We have a 659, and it more or less controls everything. I still have to use my yamaha remote to control some functions of the receiver, but overall, we are very happy. My wife used to call me at work to fire up a DVD. (We had 4 remotes) Now, all she has to do is push a single button.
You program it at the Harmony website. The setup is fairly straightforward, and customer service is really exceptional. You can actually talk to a real, live person.
The layout and feel of the remote is good. Higher order functions are accessible via buttons flanking a small LCD. The menus are simple and easy to use.