I am quite fond of my Logitech Harmony 880 remote, which I have used for a few months now. It is very easy to use and extremely easy to program given the number of components in my home theater.
The only problem I've run into (on two separate remotes) is that it will frustratingly reboot itself while in the middle of using it. After some searching, it appears this is caused by a problem with the way the battery sits in the compartment. Folding a small piece of paper and placing it between the battery and the bottom of the remote keeps the battery attached to the contacts and has eliminated the problem completely.