I have no problem paying for a Google Apps account where I actually use Google apps, but at the moment you have to have a Google Apps account to link a domain to an Appengine app. Some of our apps have two or three domains showing the same app, and because you need to have an account for each email address that Appengine sends email from, we have three or four accounts (support, noreply, accounts per domain.
So this move is going to add $600 per year to our costs - all for virtual accounts that don't actually use Google Apps at all.
Hopefully this was unintended, and Google will continue to provide free accounts for domains linked to Appengine apps - or provide another mechanism for linking and authorising sending addresses.