Here's an email from Steve Jobs to Harper Collins that forms part of the DOJ's material:
Sure, it looks like price collusion between competitors, but Apple had to do it to stop big bad Amazon! Why can't the DOJ just leave Apple alone?! /s
Edit
Judging from comments on a few sites, a lot of people don't understand why the above email is a problem. Essentially, it evidences the fact that Apple was colluding with publishers (who are all competitors) to fix prices at a higher level; schemes like this are illegal under competition law as they harm consumers and distort the market by artificially raising prices. An agreement to do this does not have to be in writing to be illegal. Depending on your jurisdiction, discussions about price by competitors (especially where those competitors form a dominant part of the market) can be per se criminal offences.
This also demonstrates a really weak compliance culture at Apple and the publishers, and the inside counsel for each should be ashamed by their failure. Organizations as large as these should make sure everyone has competition law training, and management understands that certain topics or courses of dealing when discussing matters with competitors (even at industry association meetings) are completely off-limits.