I'm not a chemist or physicist. But, a little bit of Google will confirm everything I have written. In fact, a large portion of it comes from the Wikipedia article on lithium ion batteries-
http://en.wikipedia.org/wiki/Lithium-ion_battery.
I did a fair amount of research on these batteries a while ago, when diagnosing issues with a laptop. I also have lots of personal experience with li-ion cells, as I am sure many people visiting this forum have. I feel it's safe to say that lithium ion batteries do not have a 'memory' and do not need to be conditioned. Unless they are using some new type of li-ion battery technology that I am not informed on any suggestion by HTC to discharge the battery completely is either wholly or partially incorrect or pertains strictly to calibration of how the Eris handset interprets the state of the battery.
To be accurate about this someone needs to measure the current draw of the handset in m-Ah, under typical user conditions, and measure that against the battery supplied with the device. If it's drawing, say 130 m-Ah and the phone is dying after 10 hours of usage, then the phone is using the 1300 m-Ah cell correctly (as I suspect is probably the case).
The good news is this is something that could very possibly be addressed or tweaked with future software updates. If this doesn't come to pass, one can purchase an extended life battery such as the one that will be offered by Seidio that everyone is talking about.
In any event, getting all OCD about charging your battery X amount of times is probably wasted energy.