If your site uses some sort of template so the document header is contained in one file (which is then included on every page of the site) it’s pretty simple to add a comment in that one place, and then to remove it at some time when it no longer becomes neccessary.

However, if you’re maintaining pages by hand I’d still opt for CSS-only hacks over conditional comments. And in that case I do recommend moving all your hacks to the end of the file and grouping them together, rather than leaving them scattered throughout a style sheet.