Two recent universal remotes caught my eye. It looks like Logitech has updated the 880 into the Harmony 890 (reviewed here a few months ago), adding RF device support through the use of an IR blaster. This means you'll get support for stuff like remote controlled lighting systems, overhead fans, and other non-infrared remote controlled devices. It's pricey though, going for $399 retail (the 880 is more than $100 cheaper).
Another notable new universal remote is the OpenPeak SimpleRemote. It shoots for doing everything the Harmony can do, while adding WiFi support to the device, letting you download codes, program guides, and other info directly from the internet into the remote. The one downside to the Harmony and similar remotes is you have to use a USB cable to update almost any function and often setup requires a few hours of tweaking and running between your computer and home theater system. If the SimpleRemote can let you skip that step it just might be worth checking out.