We had a strange challenge in the office last month. All of the emails that we sent to @me.com email addresses (Apple accounts), didn't get through. We checked if we had been black listed. Nothing (thank goodness). We then removed all graphics from the base. This did start to make a difference, but it was very random.
The result? After a lot of head scratching it turned out to be the .bitly links we were using. Some email clients and even social media platforms don't trust these link-shortening services as they can often shield spam/virus infested websites.
We can't track links in desktop email, but at least emails are now getting through.