When a client recently mentioned how bad and confusing the billing system's emails look when viewed in plain text format, I started investigating how to send the system notifications and invoices in both formats, as we always like to provide an option.
At this time our billing and support system offers no way to specify sending email in either HTML format or plain text format on a per client basis, only on a per type of email basis (i.e. all due invoice notices, all support replies, etc). As soon as this functionality is added to the system we use, we'll be more than happy to make this choice available to clients.
The overwhelming number of email users today prefer to send and receive HTML email. Having my roots in "old sk00l security", I do understand the security implications of accepting HTML email from unknown recipients. Though I'd never want to promote a lax attitude towards email security, the anti-virus and spam filtering combination we offer on the server is so powerful and effective (as long as you haven't changed the default settings), I can't remember the last time anything bad made it's way through to my local computer. The personal anti-virus you should be running on your own computer is a good second line of defense, though the best defense of all is basic common sense.
If you use Mozilla Thunderbird as an email client, there is a happy medium option called Simple HTML.
View -> Message Body As -> Simple HTML
.Simple HTML will only interpret the most basic HTML commands, disables JavaScript, and doesn't display remote images. This option strips out the fancy font colors and such, yet retains basic formatting without displaying the underlying HTML code. You can use the "Simple HTML" option on the fly...leaving your settings to display email in plain text and only switching to Simple HTML as needed.
The other option would be to login to your Client Portal account, and view the email there. A copy of every email the system has sent to you in the past six (6) months is kept there for your review in the Client Portal.