Justin Khoo over at freshinbox recently pointed out that Outlook.com was stripping conditional comments that were previously fair game. I recently noticed this problem myself, but strangely it didn't appear to be stripping everything, only the first instance of it. Digging a little deeper I managed to isolate the code that was causing Outlook.com to trip up and now have conditional comments working again.

Just add this little snippet after the opening body tag:

<!--[if t]><![endif]--><!--[if t]><![endif]--><!--[if t]><![endif]-->

<!--[if !mso]>
<!-- -->
<div>This should now be visible in Outlook.com again</div>

The trouble is I don't know why this works. Seems like it has something to do with the number 3. Does it work for you?