for a whole file, conditional comments are a lot simpler.
plus, conditional compilation prevents compilation of your code, and forces packaging to be done by hand. most compressors for instance, throw away comments, breaking your IE version...
<![if !IE]><script src="myExternalJS.js"></script><![endif]>
BROWSER STATS [% share]
(2013/10/31) IE7:0.5, IE8:8.6, IE9:5.3, IE10:12.3, FF:17.7, CH:41.8, SF:8.1, MOBILE:20.4