denasqu,
Hey Vancer here,
I don't know if you are as afflicted with OCD as I am, but at one point I got really anal about removing the cube...COMPLETELY. And by that I mean all the files AND all the assciated reg entries. At the time I was cooking a rom that was a customization of OMJ's 3.03 clean. It took a while to figure it all out but it is possible to remove every trace of it while cooking if you wish.
Here is an excerpt of a pm between OMJ and I where I was telling him how I accomplished this...
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I did finally get rid of the cube using your clean rom as a base
I deleted APLauncher, CustAPLauncher, MediaHubMini, and Quickdial along with a bunch of .brn files. I then had to go through the .rgu in OEMAPPS and remove all the references to those files. Built and flashed and had one refernce to App3 left in the registry that took FOREVER to find but finally did so in OEM\OperatorPKG\mixupdate_oemoperators_102.provxml . Once this was complete and I built and flashed, I no longer had the cube nor any references to it in the registry so it didn't have to be disabled
Also since I left Biotouch and TFSettings I still had touchflo scrolling. There were a few entries left in the .rgu that referenced the quickdial in a directory other than hklm\software\htc\biotouch (don't remember which one exactly), so I left them in hopes that they would be used for the HTC Home quick contacts and I'm not sure if that was the case but the quick contacts on HTC Home work and don't dissappear with a soft re-set even though there was no longer a quickdial on the cube to set them
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Give it a try next time you cook a rom and you will find no trace of the cube again, nor will you have to use 0 Kb files to replace files that aren't there
Note: This was done when OMJ was still working off a Sprint ROM rather than a Bell ROM so the reference .provxml may be a little different in the 3.09 roms
Take Care,
Vancer