I'm not making this post as an argument against conditional comments, but this is my personal reason for avoiding them. To be honest, I'm afraid of the possibility that someday, the <head> section will be filled with this:
<link rel="stylesheet" href="base-style.css" type="text/css" />
<!--[if IE]>
<link rel="stylesheet" href="ie-style.css" type="text/css" />
<[end if]-->
<!--[if FF]>
<link rel="stylesheet" href="ff-style.css" type="text/css" />
<[end if]-->
<!--[if Opera]>
<link rel="stylesheet" href="opera-style.css" type="text/css" />
<[end if]-->
<!--[if Safari]>
<link rel="stylesheet" href="safari-style.css" type="text/css" />
<[end if]-->
<!--[if Konquerer]>
<link rel="stylesheet" href="konquerer-style.css" type="text/css" />
<[end if]-->
<!--[if iCab]>
<link rel="stylesheet" href="icab-style.css" type="text/css" />
<[end if]-->
<!--[if Flock]>
<link rel="stylesheet" href="flock-style.css" type="text/css" />
<[end if]-->Conditional comments are just against my idea of how CSS should be served… and that's all I have to say about that.