Thanks to last Fall's update to the TiVo OS, there was an undocumented way to telnet commands to your TiVo that Dave Zatz describes in this post. It was a bit of a hack and not much more than a proof of concept but it looks like a few enterprising developers have created TiVo remote control apps for linux and the iPhone.
While nothing compares to a real TiVo remote in terms of functionality and ease-of-use, having an iPhone backup might be nice in the off chance you lose your remote or it's in need of repair. Cooler still is the idea of automation applications that could take advantage of of the telnet port and do away with the buggy IR blasters. I could imagine a future version of the Slingbox that could issue command over the network and confirm with a TiVo OS directly that the action took place, rather than set up an IR blaster and hope it changed the channel correctly.
Seeing people build whole apps based on discovered hacky interfaces reminds me that there is still indeed a healthy hacker culture around TiVo boxes and that if TiVo wanted to make some bold moves and document this kind of thing and any other APIs developers could use to control/tweak their TiVo devices, we'd see a nice array of innovative applications and products spring up to further enhance the TiVo experience.