Most of the discussion on this topic is in the context of Marketing Newsletters, but Mathew Patterson's Presentation on HTML Email still seems pertinent. There are a few things that are important in every communication with customers, support/system mailings included:
Branding: With a capital B. Look at this great message from Twitter:
That email's from Twitter, no doubt, it has the distinct style and professional presentation. It doesn't just look good, it fosters trust ; a plaintext email could be written by anyone, and I might be nervous to click any links provided. With a branded email there are visual cues that suggest to me that this is authentic.
Clairity: Plain text doesn't do emphasis well. With the above message there's a whole lot of text, and in plaintext it would be hard to tell what's going on. Thanks to the large, clear heirarchy of the document I determine the important things in the email:
Who sent this? Twitter.
What happened? X person is following me.
What should I do? View X's profile.
Also note the small print, deemphasized with smaller font and lower contrast. Again something plaintext just doesn't offer.