I came across an article regarding different version of win95 about how to remove IE3 from the installation process. It included changing the layout.inf to prevent it from extracting setupp.inf from the PRECOPY2.CAB, extracting the setupp.inf and removing any references to to appropriate *.inf files and then deleting theese files.
Is there any possibility to do the same with Win2000?
When I install IE6 through cmdlines.txt anyway, this would save space on the CD for other applications and you would not get any obsolete files into the installation.