Here's the first post of the topic. Apparently for the newer versions of the stock software, on HD and S3 Tivos, a telnet port is open and can be logged into. No hacking required.
Once there, codes (in text form) can be input, causing the Tivo to do just about any thing you can do with the remote. This can be scripted, to some extent.
The port was there to allow Crestron cable box's to talk to the those specific Tivo types.
Edit: After reading thru the entire thread...
Bitt's post was pointing to a bit of Phthon code that implements an on screen remote control for S3 & HD Tivos.
I tried it it seems to work as advertised.
What is lacking is the ability to query the Tivo for info. Like what's in the Now Playing list, or the guide. That's either, Unknown or "just not there".